bluuebunny/crossref_metadata_2025_split huggingface dataset:
Legacies of millennial-scale climate oscillations in contemporary biodiversity in eastern North America
Authors: Fastovich David , Radeloff Volker C. , Zuckerberg Benjamin , Williams John W. 
Published: April 2024

The Atlantic meridional overturning circulation (AMOC) has caused significant climate changes over the past 90 000 years. Prior work has hypothesized that these millennial-scale climate variations effected past and contemporary biodiversity, but the effects are understudied. Moreover, few biogeographic models have accounted for uncertainties in palaeoclimatic simulations of millennial-scale variability. We examine whether refuges from millennial-scale climate oscillations have left detectable legacies in the patterns of contemporary species richness in eastern North America. We analyse 13 palaeoclimate estimates from climate simulations and proxy-based reconstructions as predictors for the contemporary richness of amphibians, passerine birds, mammals, reptiles and trees. Results suggest that past climate changes owing to AMOC variations have left weak but detectable imprints on the contemporary richness of mammals and trees. High temperature stability, precipitation increase, and an apparent climate fulcrum in the southeastern United States across millennial-scale climate oscillations aligns with high biodiversity in the region. These findings support the hypothesis that the southeastern United States may have acted as a biodiversity refuge. However, for some taxa, the strength and direction of palaeoclimate-richness relationships varies among different palaeoclimate estimates, pointing to the importance of palaeoclimatic ensembles and the need for caution when basing biogeographic interpretations on individual palaeoclimate simulations.
This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
Range and climate niche shifts in European and North American breeding birds
Authors: Zurell Damaris , Schifferle Katrin , Herrando Sergi , Keller Verena , Lehikoinen Aleksi , Sattler Thomas , Wiedenroth Levin 
Published: April 2024

Species respond dynamically to climate change and exhibit time lags. Consequently, species may not occupy their full climatic niche during range shifting. Here, we assessed climate niche tracking during recent range shifts of European and United States (US) birds. Using data from two European bird atlases and from the North American Breeding Bird Survey between the 1980s and 2010s, we analysed range overlap and climate niche overlap based on kernel density estimation. Phylogenetic multiple regression was used to assess the effect of species morphological, ecological and biogeographic traits on range and niche metrics. European birds shifted their ranges north and north-eastwards, US birds westwards. Range unfilling was lower than expected by null models, and niche expansion was more common than niche unfilling. Also, climate niche tracking was generally lower in US birds and poorly explained by species traits. Overall, our results suggest that dispersal limitations were minor in range shifting birds in Europe and the USA while delayed extinctions from unfavourable areas seem more important. Regional differences could be related to differences in land use history and monitoring schemes. Comparative analyses of range and niche shifts provide a useful screening approach for identifying the importance of transient dynamics and time-lagged responses to climate change.
This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
A nature-positive future with biological invasions: theory, decision support and research needs
Authors: McGeoch Melodie A. , Clarke David A. , Mungi Ninad Avinash , Ordonez Alejandro 
Published: April 2024

In 2050, most areas of biodiversity significance will be heavily influenced by multiple drivers of environmental change. This includes overlap with the introduced ranges of many alien species that negatively impact biodiversity. With the decline in biodiversity and increase in all forms of global change, the need to envision the desired qualities of natural systems in the Anthropocene is growing, as is the need to actively maintain their natural values. Here, we draw on community ecology and invasion biology to (i) better understand trajectories of change in communities with a mix of native and alien populations, and (ii) to frame approaches to the stewardship of these mixed-species communities. We provide a set of premises and actions upon which a nature-positive future with biological invasions (NPF-BI) could be based, and a decision framework for dealing with uncertain species movements under climate change. A series of alternative management approaches become apparent when framed by scale-sensitive, spatially explicit, context relevant and risk-consequence considerations. Evidence of the properties of mixed-species communities together with predictive frameworks for the relative importance of the ecological processes at play provide actionable pathways to a NPF in which the reality of mixed-species communities are accommodated and managed.
This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
An assessment of the state of conservation planning in Europe
Authors: Jung Martin , Alagador Diogo , Chapman Melissa , Hermoso Virgilio , Kujala Heini , O'Connor Louise , Schinegger Rafaela , Verburg Peter H. , Visconti Piero 
Published: April 2024

Expanding and managing current habitat and species protection measures is at the heart of the European biodiversity strategy. A structured approach is needed to gain insights into such issues is systematic conservation planning, which uses techniques from decision theory to identify places and actions that contribute most effectively to policy objectives given a set of constraints. Yet culturally and historically determined European landscapes make the implementation of any conservation plans challenging, requiring an analysis of synergies and trade-offs before implementation. In this work, we review the scientific literature for evidence of previous conservation planning approaches, highlighting recent advances and success stories. We find that the conceptual characteristics of European conservation planning studies likely reduced their potential in contributing to better-informed decisions. We outline pathways towards improving the uptake of decision theory and multi-criteria conservation planning at various scales, particularly highlighting the need for (a) open data and intuitive tools, (b) the integration of biodiversity-focused conservation planning with multiple objectives, (c) accounting of dynamic ecological processes and functions, and (d) better facilitation of entry-points and co-design practices of conservation planning scenarios with stakeholders. By adopting and improving these practices, European conservation planning might become more actionable and adaptable towards implementable policy outcomes.This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
The importance of regeneration processes on forest biodiversity in old-growth forests in the Pacific Northwest
Authors: Luu Hoang , Ris Lambers Janneke Hille , Lutz James A. , Metz Margaret , Snell Rebecca S. 
Published: April 2024

Forest diversity is the outcome of multiple species-specific processes and tolerances, from regeneration, growth, competition and mortality of trees. Predicting diversity thus requires a comprehensive understanding of those processes. Regeneration processes have traditionally been overlooked, due to high stochasticity and assumptions that recruitment is not limiting for forests. Thus, we investigated the importance of seed production and seedling survival on forest diversity in the Pacific Northwest (PNW) using a forest gap model (ForClim). Equations for regeneration processes were fit to empirical data and added into the model, followed by simulations where regeneration processes and parameter values varied. Adding regeneration processes into ForClim improved the simulation of species composition, compared to Forest Inventory Analysis data. We also found that seed production was not as important as seedling survival, and the time it took for seedlings to grow into saplings was a critical recruitment parameter for accurately capturing tree species diversity in PNW forest stands. However, our simulations considered historical climate only. Due to the sensitivity of seed production and seedling survival to weather, future climate change may alter seed production or seedling survival and future climate change simulations should include these regeneration processes to predict future forest dynamics in the PNW.This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
Towards a novel biosphere in 2300: rapid and extensive global and biome-wide climatic novelty in the Anthropocene
Authors: Ordonez Alejandro , Riede Felix , Normand Signe , Svenning Jens-Christian 
Published: April 2024

Recent climate change has effectively rewound the climate clock by approximately 120 000 years and is expected to reverse this clock a further 50 Myr by 2100. We aimed to answer two essential questions to better understand the changes in ecosystems worldwide owing to predicted climate change. Firstly, we identify the locations and time frames where novel ecosystems could emerge owing to climate change. Secondly, we aim to determine the extent to which biomes, in their current distribution, will experience an increase in climate-driven ecological novelty. To answer these questions, we analysed three perspectives on how climate changes could result in novel ecosystems in the near term (2100), medium (2200) and long term (2300). These perspectives included identifying areas where climate change could result in new climatic combinations, climate isoclines moving faster than species migration capacity and current environmental patterns being disaggregated. Using these metrics, we determined when and where novel ecosystems could emerge. Our analysis shows that unless rapid mitigation measures are taken, the coverage of novel ecosystems could be over 50% of the land surface by 2100 under all change scenarios. By 2300, the coverage of novel ecosystems could be above 80% of the land surface. At the biome scale, these changes could mean that over 50% of locations could shift towards novel ecosystems, with the majority seeing these changes in the next few decades. Our research shows that the impact of climate change on ecosystems is complex and varied, requiring global action to mitigate and adapt to these changes. This article is part of the theme issue ‘Biodiversity dynamics and stewardship in a transforming biosphere’.
This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
Global indicators of the environmental impacts of invasive alien species and their information adequacy
Authors: Henriksen Marie V. , Arlé Eduardo , Pili Arman , Clarke David A. , García-Berthou Emili , Groom Quentin , Lenzner Bernd , Meyer Carsten , Seebens Hanno , Tingley Reid , Winter Marten , McGeoch Melodie A. 
Published: April 2024

Monitoring the extent to which invasive alien species (IAS) negatively impact the environment is crucial for understanding and mitigating biological invasions. Indeed, such information is vital for achieving Target 6 of the Kunming–Montreal Global Biodiversity Framework. However, to-date indicators for tracking the environmental impacts of IAS have been either lacking or insufficient. Capitalizing on advances in data availability and impact assessment protocols, we developed environmental impact indicators to track realized and potential impacts of IAS. We also developed an information status indicator to assess the adequacy of the data underlying the impact indicators. We used data on 75 naturalized amphibians from 82 countries to demonstrate the indicators at a global scale. The information status indicator shows variation in the reliability of the data and highlights areas where absence of impact should be interpreted with caution. Impact indicators show that growth in potential impacts are dominated by predatory species, while potential impacts from both predation and disease transmission are distributed worldwide. Using open access data, the indicators are reproducible and adaptable across scales and taxa and can be used to assess global trends and distributions of IAS, assisting authorities in prioritizing control efforts and identifying areas at risk of future invasions.This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
Future changes in society and climate may strongly shape wild large-herbivore faunas across Europe
Authors: Davoli Marco , Svenning Jens-Christian 
Published: April 2024

Restoring wild communities of large herbivores is critical for the conservation of biodiverse ecosystems, but environmental changes in the twenty-first century could drastically affect the availability of habitats. We projected future habitat dynamics for 18 wild large herbivores in Europe and the relative future potential patterns of species richness and assemblage mean body weight considering four alternative scenarios of socioeconomic development in human society and greenhouse gas emissions (SSP1–RCP2.6, SSP2–RCP4.5, SSP3–RCP7.0, SSP5–RCP8.5). Under SSP1–RCP2.6, corresponding to a transition towards sustainable development, we found stable habitat suitability for most species and overall stable assemblage mean body weight compared to the present, with an average increase in species richness (in 2100: 3.03 ± 1.55 compared to today′s 2.25 ± 1.31 species/area). The other scenarios are generally unfavourable for the conservation of wild large herbivores, although under the SSP5–RCP8.5 scenario there would be increase in species richness and assemblage mean body weight in some southern regions (e.g. + 62.86 kg mean body weight in Balkans/Greece). Our results suggest that a shift towards a sustainable socioeconomic development would overall provide the best prospect of our maintaining or even increasing the diversity of wild herbivore assemblages in Europe, thereby promoting trophic complexity and the potential to restore functioning and self-regulating ecosystems.This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
Predicting the responses of European grassland communities to climate and land cover change
Authors: Liu Chang , Van Meerbeek Koenraad 
Published: April 2024

European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species.This article is part of the theme issue ‘Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere’.
Distinct genomic and immunologic tumor evolution in germlineTP53-driven breast cancers
Authors: Boruah Nabamita , Hoyos David , Moses Renyta , Hausler Ryan , Desai Heena , Le Anh N , Good Madeline , Kelly Gregory , Raghavakaimal Ashvathi , Tayeb Maliha , Narasimhamurthy Mohana , Doucette Abigail , Gabriel Peter , Feldman Michael J. , Park Jinae , Lopez de Rodas Miguel , Schalper Kurt A. , Goldfarb Shari B. , Nayak Anupma , Levine Arnold J. , Greenbaum Benjamin D. , Maxwell Kara N. 
Published: April 2024

AbstractPathogenic germlineTP53alterations cause Li-Fraumeni Syndrome (LFS), and breast cancer is the most common cancer in LFS females. We performed first of its kind multimodal analysis of LFS breast cancer (LFS-BC) compared to sporadic premenopausal BC. Nearly all LFS-BC underwent biallelic loss ofTP53with no recurrent oncogenic variants exceptERBB2(HER2) amplification. Compared to sporadic BC,in situand invasive LFS-BC exhibited a high burden of short amplified aneuploid segments (SAAS). Pro-apoptotic p53 target genesBAXandTP53I3failed to be up-regulated in LFS-BC as was seen in sporadic BC compared to normal breast tissue. LFS-BC had lower CD8+ T-cell infiltration compared to sporadic BC yet higher levels of proliferating cytotoxic T-cells. Within LFS-BC, progression fromin situto invasive BC was marked by an increase in chromosomal instability with a decrease in proliferating cytotoxic T-cells. Our study uncovers critical events in mutant p53-driven tumorigenesis in breast tissue.
Glenn circulation causes early and progressive shunting in a surgical model of pulmonary arteriovenous malformations
Authors: Wan Tina , Rousseau Henry , Mattern Carol , Tabor Madeline , Hodges Matthew R. , Ramchandran Ramani , Spearman Andrew D. 
Published: April 2024

AbstractBackgroundPulmonary arteriovenous malformations (PAVMs) universally develop in patients with single ventricle congenital heart disease (CHD). Single ventricle PAVMs have been recognized for over 50 years, yet they are poorly understood, and we lack any medical therapies. To improve our understanding of single ventricle PAVM initiation and progression, we developed a surgical rat model of Glenn circulation and characterized PAVM physiology over multiple time points.MethodsUsing adult rats, we performed a left thoracotomy and end-to-end anastomosis of the left superior vena cava to the left pulmonary artery (unilateral Glenn), or sham surgical control. To assess for PAVM physiology in the left lung, we quantified intrapulmonary shunting using two independent methods (bubble echocardiography and fluorescent microsphere injection) at 2 weeks, 2 months, and 6 months. Additionally, we performed arterial blood gas measurements to assess oxygenation and plethysmography to assess ventilation.ResultsWe identified pathologic intrapulmonary shunting by bubble echocardiography as early as 2 weeks post-Glenn surgery, and shunting continued chronically at 2- and 6-months post-Glenn. Shunting also progressed over time, demonstrated by increased shunting of 10µm microspheres at 6 months. Shunting was accompanied by mildly decreased arterial oxygenation, but there were no differences in ventilation as quantified by plethysmography.ConclusionsOur surgical animal model of unilateral Glenn circulation re-creates the clinical condition of single ventricle PAVMs with early and progressive intrapulmonary shunting. This model is poised to characterize single ventricle PAVM pathophysiology and lead to mechanistic and therapeutic discovery.Graphic Abstract
Assessing the Impact of use of HIV self-testing on the incidence of HIV Infection in Nigeria: a systematic review and meta-analysis
Authors: Eleje George Uchenna , Emmanuel Godwin Omokhagbo , Akinsolu Folahanmi Tomiwa , Foláyan Morẹ́nikẹ́ Oluwátóyìn 
Published: April 2024

AbstractBackgroundHuman immunodeficiency virus (HIV) self-testing tool is a widely adopted tool in Nigeria. However, there is little known about its impact in reducing HIV infection rates in Nigeria. This review aims to assess the impact of the use of HIV self-testing on the incidence of HIV infections in the country.MethodsThis was a systematic review and meta-analysis. Studies conducted in Nigeria on HIV self- testing with or without comparison to other HIV tests were included. The primary outcomes considered were the detection rate of new HIV cases and the acceptability (uptake) rate for HIV self-testing. Secondary outcomes were the usability rate, repeat testing rate, willingness rate, awareness rate, incidence of social harm, and incidence of high-risk behaviour. Electronic databases (PubMed/Medline, Web of Science, Scopus, CINAHL, and Cochrane Library) and Google Scholar were searched for relevant studies. Searches were conducted till December 2, 2023. Pooled estimates were calculated using a random-effects model with the DerSimonian Laird method. Heterogeneity was analyzed using the I2test, and risk of bias was assessed with the Hoy and colleagues’ scale. Meta-analysis was conducted where possible. The protocol was registered with PROSPERO (CRD42023479752).ResultsEight studies, encompassing 7,556 participants, met the inclusion criteria. The overall risk of bias for the included studies was adjudged low. The detection rate of HIV self-testing for new HIV cases was 25.78% (95% CI: 0.90-50.66, I2:100.0), acceptability (uptake) rate was 56.92% (95% CI: 26.54-87.30, I2:100.0), and repeat testing rate was 20.10% (95% CI: -11.44-51.65, I2:100.0). Usability rate, willingness rate, awareness rate, and incidence of high-risk behaviour were reported in one study respectively, with no information on the incidence of social harm. Sensitivity analysis was done, and subgroup analyses could not be estimated due to insufficient data.ConclusionsThe use of HIV self-testing test kits in Nigeria showed a high detection rate of new HIV cases, moderate acceptability, but low repeat testing rates. However, the evidence is limited. Larger, higher-quality studies are essential to explore the broader impact of HIV self-testing on reducing HIV incidence in Nigeria.