93 results on '"Schmucki R"'
Search Results
2. Mechanisms underpinning community stability along a latitudinal gradient: Insights from a niche-based approach
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Evans, L.C., Melero, Y., Schmucki, R., Boersch-Supan, P.H., Brotons, L., Fontaine, C., Jiguet, F., Kuussaari, M., Massimino, D., Robinson, R.A., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., van Turnhout, C.A.M., Oliver, T.H., Evans, L.C., Melero, Y., Schmucki, R., Boersch-Supan, P.H., Brotons, L., Fontaine, C., Jiguet, F., Kuussaari, M., Massimino, D., Robinson, R.A., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., van Turnhout, C.A.M., and Oliver, T.H.
- Abstract
At large scales, the mechanisms underpinning stability in natural communities may vary in importance due to changes in species composition, mean abundance, and species richness. Here we link species characteristics (niche positions) and community characteristics (richness and abundance) to evaluate the importance of stability mechanisms in 156 butterfly communities monitored across three European countries and spanning five bioclimatic regions. We construct niche-based hierarchical structural Bayesian models to explain first differences in abundance, population stability, and species richness between the countries, and then explore how these factors impact community stability both directly and indirectly (via synchrony and population stability). Species richness was partially explained by the position of a site relative to the niches of the species pool, and species near the centre of their niche had higher average population stability. The differences in mean abundance, population stability, and species richness then influenced how much variation in community stability they explained across the countries. We found, using variance partitioning, that community stability in Finnish communities was most influenced by community abundance, whereas this aspect was unimportant in Spain with species synchrony explaining most variation; the UK was somewhat intermediate with both factors explaining variation. Across all countries, the diversity–stability relationship was indirect with species richness reducing synchrony which increased community stability, with no direct effects of species richness. Our results suggest that in natural communities, biogeographical variation observed in key drivers of stability, such as population abundance and species richness, leads to community stability being limited by different factors and that this can partially be explained due to the niche characteristics of the European butterfly assemblage.
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- 2023
3. Bioclimatic context of species' populations determines community stability
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Evans, Luke Christopher, Melero, Yolanda, Schmucki, R., Boersch-Supan, Philipp H., Brotons, L., Fontaine, Colin, Turnhout, C.A.M. van, Oliver, T.H., Evans, Luke Christopher, Melero, Yolanda, Schmucki, R., Boersch-Supan, Philipp H., Brotons, L., Fontaine, Colin, Turnhout, C.A.M. van, and Oliver, T.H.
- Abstract
17 juni 2022, Contains fulltext : 251782.pdf (Publisher’s version ) (Open Access)
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- 2022
4. LukeChristopherEvans/BioclimaticContextCommunityStability: V2 BioclimaticContextCommunityStability (v1.0.2-beta)
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Evans, L.C., Melero, Y., Schmucki, R., Boersch-Supan, P.H., Brotons, L., Fontaine, C., Jiguet, F., Kuussaari, M., Massimino, D., Robinson, R.A., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., van Turnhout, C.A.M., Oliver, T.H., Evans, L.C., Melero, Y., Schmucki, R., Boersch-Supan, P.H., Brotons, L., Fontaine, C., Jiguet, F., Kuussaari, M., Massimino, D., Robinson, R.A., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., van Turnhout, C.A.M., and Oliver, T.H.
- Abstract
Aim It is important to understand the factors affecting community stability because ecosystem function is increasingly at risk from biodiversity loss. Here, we evaluate how a key factor, the position of local environmental conditions within the thermal range of the species, influences the stability of butterfly communities at a continental scale. Location Spain, UK and Finland. Time period 1999–2017. Major taxa studied Butterflies. Methods We tested the following hypotheses about how species responses to temperature anomalies aggregate to influence stability: Hypothesis 1, species have contrasting responses to local temperature anomalies at opposing edges of their thermal range; hypothesis 2, communities with central thermal range positions have higher community stability; and the impacts of thermal range position on community stability are driven by hypothesis 3, population asynchrony, or hypothesis 4, additive population stability. Data were analysed at 876 sites for 157 species. Results We found some support for hypothesis 1, because there were interactions between thermal range and response to temperature anomalies such that species at different range edges could provide weak compensatory dynamics. However, responses were nonlinear, suggesting strong declines with extreme anomalies, particularly at the hot range edge. Hypothesis 2 was supported in part, because community stability increased with central thermal range positions and declined at the edges, after accounting for species richness and community abundance. Thermal range position was weakly correlated with asynchrony (hypothesis 3) and population stability (hypothesis 4), although species richness and population abundance had larger impacts. Main conclusions Future extreme heat events will be likely to impact species negatively across their thermal range, but might be particularly impactful on populations at the hottest end of the thermal range. Thermal range position influenced community stability becau
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- 2022
5. European grassland butterfly indicator 1990-2020 Technical report. Butterfly Conservation Europe & SPRING/eBMS
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van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C.G., Åström, S., Balalaikins, M., Barea-Azcón, J.M., Bonelli, S., Botham, M., Cancela, J.P., Collins, S., De Flores, M., Dapporto, L., Dopagne, C., Dziekanska, I., Escobés, R., Faltynek Fric, Z., Fernández-García, J.M., Fontaine, B., Glogovčan, P., Gracianteparaluceta, A., Harpke, Alexander, Harrower, C., Heliölä, J., Houard, X., Judge, M., Kolev, Z., Komac, B., Kühn, Elisabeth, Kuussaari, M., Lang, A., Lysaght, L., Maes, D., McGowan, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Monteiro, E., Munguira, M.L., Musche, Martin, Olivares, F.J., Õunap, E., Ozden, O., Pavlíčko, A., Pendl, M., Pettersson, L.B., Rákosy, L., Roth, T., Rüdisser, J., Šašić, M., Scalercio, S., Settele, Josef, Sielezniew, M., Sobczyk-Moran, G., Stefanescu, C., Švitra, G., Szabadfalvi, A., Tiitsaar, A., Titeux, N., Tzirkalli, E., Ubach, A., Verovnik, R., Vray, S., Warren, M.S., Wynhoff, I., Roy, D.B., van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C.G., Åström, S., Balalaikins, M., Barea-Azcón, J.M., Bonelli, S., Botham, M., Cancela, J.P., Collins, S., De Flores, M., Dapporto, L., Dopagne, C., Dziekanska, I., Escobés, R., Faltynek Fric, Z., Fernández-García, J.M., Fontaine, B., Glogovčan, P., Gracianteparaluceta, A., Harpke, Alexander, Harrower, C., Heliölä, J., Houard, X., Judge, M., Kolev, Z., Komac, B., Kühn, Elisabeth, Kuussaari, M., Lang, A., Lysaght, L., Maes, D., McGowan, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Monteiro, E., Munguira, M.L., Musche, Martin, Olivares, F.J., Õunap, E., Ozden, O., Pavlíčko, A., Pendl, M., Pettersson, L.B., Rákosy, L., Roth, T., Rüdisser, J., Šašić, M., Scalercio, S., Settele, Josef, Sielezniew, M., Sobczyk-Moran, G., Stefanescu, C., Švitra, G., Szabadfalvi, A., Tiitsaar, A., Titeux, N., Tzirkalli, E., Ubach, A., Verovnik, R., Vray, S., Warren, M.S., Wynhoff, I., and Roy, D.B.
- Abstract
Butterfly monitoring enjoys a growing popularity in Europe, mainly supported by Butterfly Conservation Europe (BCE) and its partners. While Butterfly Monitoring Schemes are present in a growing number of countries and new ones are being initiated in many places, long time-series are currently only available for a limited number of countries. For the indicators in this report, we used data from 22 countries (Figure 1): Andorra, Austria, Belgium, Czech Republic, Estonia, Finland, France, Germany, Hungary, Ireland, Jersey, Latvia, Lithuania, Luxembourg, Norway, Romania, Slovenia, Spain, Sweden, Switzerland, The Netherlands and the United Kingdom.The indicators use field data up to and including the 2020 field season. The method for calculating indicators has been greatly improved and enhanced. During 2020, more than 2,500 standardised butterfly transects distributed across 22 monitoring schemes were used to inform the EU27 Grassland Butterfly Indicator and almost 5,000 from 25 schemes for the European Grassland Butterfly Indicator (Figure 2). Since 1990 over 6,350 and 11,500 separate transects have contributed to the EU27 and Europe indicators, respectively.
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- 2022
6. Bioclimatic context of species' populations determines community stability
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Evans, L.C., Melero, Y., Schmucki, R., Boersch-Supan, P.H., Brotons, L., Fontaine, C., Jiguet, F., Kuussaari, M., Massimino, D., Robinson, R.A., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., van Turnhout, C.A.M., Oliver, T.H., Evans, L.C., Melero, Y., Schmucki, R., Boersch-Supan, P.H., Brotons, L., Fontaine, C., Jiguet, F., Kuussaari, M., Massimino, D., Robinson, R.A., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., van Turnhout, C.A.M., and Oliver, T.H.
- Abstract
Aim It is important to understand the factors affecting community stability because ecosystem function is increasingly at risk from biodiversity loss. Here, we evaluate how a key factor, the position of local environmental conditions within the thermal range of the species, influences the stability of butterfly communities at a continental scale. Location Spain, UK and Finland. Time period 1999–2017. Major taxa studied Butterflies. Methods We tested the following hypotheses about how species responses to temperature anomalies aggregate to influence stability: Hypothesis 1, species have contrasting responses to local temperature anomalies at opposing edges of their thermal range; hypothesis 2, communities with central thermal range positions have higher community stability; and the impacts of thermal range position on community stability are driven by hypothesis 3, population asynchrony, or hypothesis 4, additive population stability. Data were analysed at 876 sites for 157 species. Results We found some support for hypothesis 1, because there were interactions between thermal range and response to temperature anomalies such that species at different range edges could provide weak compensatory dynamics. However, responses were nonlinear, suggesting strong declines with extreme anomalies, particularly at the hot range edge. Hypothesis 2 was supported in part, because community stability increased with central thermal range positions and declined at the edges, after accounting for species richness and community abundance. Thermal range position was weakly correlated with asynchrony (hypothesis 3) and population stability (hypothesis 4), although species richness and population abundance had larger impacts. Main conclusions Future extreme heat events will be likely to impact species negatively across their thermal range, but might be particularly impactful on populations at the hottest end of the thermal range. Thermal range position influenced community stability becau
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- 2022
7. Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data
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Pellissier, V., Schmucki, R., Pe'er, G., Aunins, A., Brereton, T.M., Brotons, L., Carnicer, J., Chodkiewicz, T., Chylarecki, P., del Moral, J.C., Escandell, V., Evans, D M, Foppen, R.P.B., Harpke, A., Heliölä, J., Herrando, S., Kuussaari, M., Kühn, E., Lehikoinen, A., Lindström, Å., Moshøj, C.M., Musche, M., Noble, D., Oliver, T.H., Reif, J., Richard, D., Roy, D.B., Schweiger, O., Settele, J., Stefanescu, C., Teufelbauer, N., Touroult, J., Trautmann, S., van Strien, A.J., van Swaay, C.A.M., Turnhout, C.A.M. van, Vermouzek, Z., Voříšek, P., Jiguet, F., Julliard, R., Pellissier, V., Schmucki, R., Pe'er, G., Aunins, A., Brereton, T.M., Brotons, L., Carnicer, J., Chodkiewicz, T., Chylarecki, P., del Moral, J.C., Escandell, V., Evans, D M, Foppen, R.P.B., Harpke, A., Heliölä, J., Herrando, S., Kuussaari, M., Kühn, E., Lehikoinen, A., Lindström, Å., Moshøj, C.M., Musche, M., Noble, D., Oliver, T.H., Reif, J., Richard, D., Roy, D.B., Schweiger, O., Settele, J., Stefanescu, C., Teufelbauer, N., Touroult, J., Trautmann, S., van Strien, A.J., van Swaay, C.A.M., Turnhout, C.A.M. van, Vermouzek, Z., Voříšek, P., Jiguet, F., and Julliard, R.
- Abstract
Contains fulltext : 216802.pdf (publisher's version ) (Closed access), The European Union's Natura 2000 (N2000), is one of the largest international networks of protected areas. One of its aims is to secure the status of a pre-determined set of (targeted) bird and butterfly species. However, also non-target species may benefit from N2000. We evaluated how the terrestrial component of this network relates to the abundance of non-targeted, more common bird and butterfly species using data from long-term volunteer-based monitoring programs in 9,602 sites for birds and 2,001 sites for butterflies. In almost half of the 155 bird species assessed, and particularly among woodland specialists, abundance increased with the proportion of N2000 sites in the landscape. The corresponding positive relationship was found for 27 of the 104 butterfly species, although most of these species were generalists. These positive relationships disappeared for most of the species when land-cover covariates were taken into account, hinting that land-cover is a primary factor defining the positive effects of the N2000 network. The increase in abundance with N2000 was correlated with the specialization index for bird species, but not for butterfly species. Although the N2000 network supports higher abundance of a large spectrum of species, the low number of specialist butterfly species showing a positive association stresses the need to implement management plan improving the quality of habitats of N2000 areas potentially harboring openland butterfly specialists. For a better understanding of the processes involved, we advocate for a standardized collection of data on N2000 sites. Article impact statement: Across Europe the abundance of a majority of nontarget birds and a quarter of nontarget butterflies increased with Natura 2000 coverage. This article is protected by copyright. All rights reserved
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- 2020
8. Assessing Butterflies in Europe. Executive summary
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Roy, D.B., Bourn, N., Collins, S., Dennis, E.B., Schmucki, R., Settele, J., Sevilleja, C.G., Van Swaay, C.A.M., Wynhoff, I., Roy, D.B., Bourn, N., Collins, S., Dennis, E.B., Schmucki, R., Settele, J., Sevilleja, C.G., Van Swaay, C.A.M., and Wynhoff, I.
- Abstract
1. The Assessing Butterflies in Europe (ABLE) project was an EU Parliamentary Pilot project with a duration of two years (beginning of December 2019 to the end of November 2020) and received €800,000 of funding via a service contract with Directorate General Environment. 2. The mandate and rationale from the EU Parliament was: “The project aims at developing a suite of EU Lepidoptera indicators which can help improve conservation measure and assess progress in implementing EU policies and legislation such as the EU Biodiversity Strategy to 2020 and the EU Habitats Directive. Besides providing a highly relevant indicator for measuring progress in terms of managing and restoring Natura 2000 sites, it would also contribute to monitoring progress on Target 3 of the EU Biodiversity Strategy, which aims to increase the contribution of agriculture and forestry to maintaining and enhancing biodiversity. In particular, the pilot should deliver a representative indicator to help monitor the impact of the Common Agricultural Policy on grassland biodiversity. It will also provide data to produce a climate change indicator, thereby contributing to the ongoing revision of climate change adaptation strategies. Indicators will also be possible for woodland, wetland and urban habitats.” 3. The ABLE project was delivered by a consortium of the UK Centre for Ecology & Hydrology, Butterfly Conservation Europe, Butterfly Conservation UK, De Vlinderstichting and HelmholtzZentrum für Umweltforschung GmbH – UFZ. Considerable in-kind contributions were provided by Butterfly Conservation partners across Europe. 4. There is mounting evidence of widespread declines in the diversity and abundance of insects across the globe. The ABLE project is particularly timely in helping to develop capacity for monitoring of insects and assessing the status of butterflies in the EU. 5. There are 482 butterfly species in Europe (451 occurring within the EU27), breeding in a wide range of habitats. Butterflie
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- 2020
9. Tools to support butterfly monitoring and analysis. Technical report
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Schmucki, R., Sevilleja, C., Dennis, E.B., Harrower, C.A., Kazlauskis, K., Rathod, B., van Breda, G., van Breda, J., Van Swaay, C.A.M., Roy, D.B., Schmucki, R., Sevilleja, C., Dennis, E.B., Harrower, C.A., Kazlauskis, K., Rathod, B., van Breda, G., van Breda, J., Van Swaay, C.A.M., and Roy, D.B.
- Abstract
This report summarises the work within ABLE to contribute to the development of a unified system of validated and standardised butterfly counts from across European monitoring schemes. The primary aim is to provide the technical infrastructure to support the development of butterfly monitoring schemes within EU member states and regular reports on butterfly indicators and to enrich research on biodiversity. To achieve this objective, this report summarises work on the following activities: 1. Produce an effective database for butterfly monitoring records to ensure secure long-term data storage and provide with the capability to produce a suite of butterfly indicators; 2. Establish legal data-sharing agreements with existing monitoring schemes to clarify intellectual property rights and rights of access to data; 3. Gather data annually from existing monitoring schemes, standardise and validate counts, populate database; 4. Extend online data entry systems to allow new countries to submit data efficiently and in a standard format; 5. Develop and test a mobile application for capturing timed counts of butterflies across Europe, supporting a new protocol developed in this project; 6. Provide training for monitoring scheme volunteers and scheme co-ordinators in the use of the online data entry system and data analysis tools; 7. Provide tools, training and online resources for calculating national butterfly population trends; 8. Make BMS records and metadata available in a standard and validated format for research as appropriate.
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- 2020
10. Butterfly indicators 1990-2018. Technical report
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Van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C.G., Aghababyan, K., Astrom, S., Balalaikins, M., Bonelli, S., Botham, M., Bourn, N., Brereton, T., Cancela, J.P., Carlisle, B., Collins, S., Dopagne, C., Dziekanska, I., Escobes, R., Faltynek Fric, Z., Feldman, R., Fernandez-Garcia, J.M., Fontaine, B., Goloshchapova, S., Gracianteparaluceta, A., Harpke, A., Harrower, C., Heliola, J., Khanamirian, G., Kolev, Z., Komac, B., Krenn, H., Kuhn, E., Lang, A., Leopold, P., Lysaght, L., Maes, D., McGowan, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Monteiro, E., Munguira, M.L., Musche, M., Ounap, E., Ozden, O., Paramo, F., Pavlicko, A., Petterson, L.B., Piqueray, J., Prokofev, I., Rakosy, L., Roth, T., Rudisser, J., Sasic, M., Settele, J., Sielezniew, M., Stefanescu, C., Svitra, G., Szabadfalvi, A., Teixeira, S.M., Tiitsaar, A., Tzirkalli, E., Verovnik, R., Warren, M.S., Wynhoff, I., Roy, D.B., Van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C.G., Aghababyan, K., Astrom, S., Balalaikins, M., Bonelli, S., Botham, M., Bourn, N., Brereton, T., Cancela, J.P., Carlisle, B., Collins, S., Dopagne, C., Dziekanska, I., Escobes, R., Faltynek Fric, Z., Feldman, R., Fernandez-Garcia, J.M., Fontaine, B., Goloshchapova, S., Gracianteparaluceta, A., Harpke, A., Harrower, C., Heliola, J., Khanamirian, G., Kolev, Z., Komac, B., Krenn, H., Kuhn, E., Lang, A., Leopold, P., Lysaght, L., Maes, D., McGowan, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Monteiro, E., Munguira, M.L., Musche, M., Ounap, E., Ozden, O., Paramo, F., Pavlicko, A., Petterson, L.B., Piqueray, J., Prokofev, I., Rakosy, L., Roth, T., Rudisser, J., Sasic, M., Settele, J., Sielezniew, M., Stefanescu, C., Svitra, G., Szabadfalvi, A., Teixeira, S.M., Tiitsaar, A., Tzirkalli, E., Verovnik, R., Warren, M.S., Wynhoff, I., and Roy, D.B.
- Abstract
There is mounting evidence of widespread declines in the diversity and abundance of insects from across the globe (Sanchez-Bayo and Wyckhuys 2019, Seibold et al. 2019, van Klink et al. 2020, Wagner 2020). This gives a stark warning for the perilous state of biodiversity (Diaz et al. 2019), and demonstrates that addressing the gap in knowledge of the status of insects is vital (Cardoso et al. 2020, Samways et al. 2020). Insects are estimated to comprise more than half of all described species and are a dominant component of biodiversity in most ecosystems (Bar-On et al. 2018). Insects also provide a crucial role in the functioning of ecosystems. They are not only related to the supply of many ecosystem services such as pollination, biological control, soil fertility regulation and diverse cultural ecosystem services but also to disservices such as damage to crops and spread of diseases to livestock and humans (Gutierrez-Arellano and Mulligan 2018, Noriega et al. 2018). There is a pressing need to assess the status of insects to set and evaluate conservation targets. At the Convention on Biological Diversity (CBD) meeting in Nagoya (Japan), the Strategic Plan for Biodiversity 2011-2020 was adopted. It proposed five goals and 20 "Aichi" biodiversity targets. In line with this plan, a new EU biodiversity strategy was adopted by the European Commission in May 2011. This strategy provided a framework for the EU to meet its biodiversity targets and global commitments as a party to the CBD. The Headline Target in the existing EU Biodiversity Strategy 2020 is to halt the loss of biodiversity and the degradation of ecosystem services in the EU by 2020, and restore them, in so far as feasible, while stepping up the EU contribution to averting global biodiversity loss. Under Target 3A the EU is committed to increasing the contribution of agriculture to biodiversity recovery. Further, the EU Biodiversity Strategy 2030 includes the development of a coherent framework for monitori
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- 2020
11. European Butterfly Monitoring Scheme (eBMS): network development. Technical report
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Sevilleja, C.G., Collins, S., Warren, M.S., Wynhoff, I., Van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Barea Azcon, J.M., Bonelli, S., Bourn, N., Cassar, L.F., de Arce Crespo, J.I., Dziekanska, I., Faltynek Fric, Z., Kolev, Z., Krenn, H., Lehner, D., Monteiro, E., Munguira, M.L., Ozden, O., Pavlicko, A., Pendl, M., Rudisser, J., Sasic, M., Sielezniew, M., Settele, J., Szabadfalvi, A., Teixeira, S.M., Tzirkalli, E., Roy, D.B., Sevilleja, C.G., Collins, S., Warren, M.S., Wynhoff, I., Van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Barea Azcon, J.M., Bonelli, S., Bourn, N., Cassar, L.F., de Arce Crespo, J.I., Dziekanska, I., Faltynek Fric, Z., Kolev, Z., Krenn, H., Lehner, D., Monteiro, E., Munguira, M.L., Ozden, O., Pavlicko, A., Pendl, M., Rudisser, J., Sasic, M., Sielezniew, M., Settele, J., Szabadfalvi, A., Teixeira, S.M., Tzirkalli, E., and Roy, D.B.
- Abstract
1. The ABLE EU Pilot Project was initiated in 2018 to collate butterfly monitoring data across Europe, to facilitate the start of new schemes in the EU, and to develop indicators to help policy evaluation. This report summarises the work on developing the monitoring network (Task 2). 2. There are some 451 butterfly species occurring in the Member States of the EU(27), breeding in a wide range of habitats. Butterflies react quickly to change and are considered to be good biological indicators, especially other insects and pollinators. Monitoring butterflies can help shed light on changes in these important groups. 3. Standard methods of monitoring butterflies are well established, based on fixed routes (transects), which allow citizen scientists to estimate the relative abundance of butterflies. 4. Prior to ABLE, several countries contributed butterfly monitoring data to the European Butterfly Monitoring Scheme (eBMS), but they were concentrated in central and western Europe. Large parts of southern and eastern Europe had no regular scheme. Three groups were prioritised for action: six to eight EU countries which had a good probability of establishing a scheme; recently started schemes that required further support; and countries where longer term activities were needed to develop monitoring. 5. As a result of the two-year project, ten EU(27) countries have started new citizen Science Butterfly Monitoring Schemes - Italy, Portugal, Hungary, Austria, Cyprus in 2019 and Poland, Bulgaria, Malta, Czech and Croatia in 2020; seven of these have joined the eBMS data network. Further details are in Annex 2. 6. A suite of support materials has been produced, including a Butterfly Transect Manual, which has been translated into six languages and a series of regional butterfly identification guides. Videos have been made explaining how to count butterflies on a transect and PowerPoint presentations have been made available in several languages. 7. More than 20 workshops and tra
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- 2020
12. Data Integration for Large-Scale Models of Species Distributions
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Isaac, NJB, Jarzyna, MA, Keil, P, Dambly, LI, Boersch-Supan, PH, Browning, E, Freeman, SN, Golding, N, Guillera-Arroita, G, Henrys, PA, Jarvis, S, Lahoz-Monfort, J, Pagel, J, Pescott, OL, Schmucki, R, Simmonds, EG, O'Hara, RB, Isaac, NJB, Jarzyna, MA, Keil, P, Dambly, LI, Boersch-Supan, PH, Browning, E, Freeman, SN, Golding, N, Guillera-Arroita, G, Henrys, PA, Jarvis, S, Lahoz-Monfort, J, Pagel, J, Pescott, OL, Schmucki, R, Simmonds, EG, and O'Hara, RB
- Abstract
With the expansion in the quantity and types of biodiversity data being collected, there is a need to find ways to combine these different sources to provide cohesive summaries of species' potential and realized distributions in space and time. Recently, model-based data integration has emerged as a means to achieve this by combining datasets in ways that retain the strengths of each. We describe a flexible approach to data integration using point process models, which provide a convenient way to translate across ecological currencies. We highlight recent examples of large-scale ecological models based on data integration and outline the conceptual and technical challenges and opportunities that arise.
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- 2020
13. Assessing butterflies in Europe – European Butterfly Monitoring Scheme - Network development: Technical report
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Sevilleja, C.G., Collins, S., Warren, M.S., Wynhoff, I., van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Barea Azcón, J.M., Bonelli, S., Bourn, N., Cassar, L.F., de Arce Crespo, J.I., Dziekańska, I., Faltynek Fric, Z., Kolev, Z., Krenn, H., Lehner, D., Monteiro, E., Munguira, M.L., Özden, Ö., Pavlíčko, A., Pendl, M., Rüdisser, J., Šašić, M., Sielezniew, M., Settele, Josef, Szabadfalvi, A., Teixeira, S.M., Tzirkalli, E., Roy, D.B., Sevilleja, C.G., Collins, S., Warren, M.S., Wynhoff, I., van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Barea Azcón, J.M., Bonelli, S., Bourn, N., Cassar, L.F., de Arce Crespo, J.I., Dziekańska, I., Faltynek Fric, Z., Kolev, Z., Krenn, H., Lehner, D., Monteiro, E., Munguira, M.L., Özden, Ö., Pavlíčko, A., Pendl, M., Rüdisser, J., Šašić, M., Sielezniew, M., Settele, Josef, Szabadfalvi, A., Teixeira, S.M., Tzirkalli, E., and Roy, D.B.
- Abstract
Executive Summary 1. The ABLE EU Pilot Project was initiated in 2018 to collate butterfly monitoring data across Europe, to facilitate the start of new schemes in the EU, and to develop indicators to help policy evaluation. This report summarises the work on developing the monitoring network (Task 2). 2. There are some 451 butterfly species occurring in the Member States of the EU(27), breeding in a wide range of habitats. Butterflies react quickly to change and are considered to be good biological indicators, especially other insects and pollinators. Monitoring butterflies can help shed light on changes in these important groups. 3. Standard methods of monitoring butterflies are well established, based on fixed routes (transects), which allow citizen scientists to estimate the relative abundance of butterflies. 4. Prior to ABLE, several countries contributed butterfly monitoring data to the European Butterfly Monitoring Scheme (eBMS), but they were concentrated in central and western Europe. Large parts of southern and eastern Europe had no regular scheme. Three groups were prioritised for action: six to eight EU countries which had a good probability of establishing a scheme; recently started schemes that required further support; and countries where longer term activities were needed to develop monitoring. 5. As a result of the two-year project, ten EU(27) countries have started new citizen Science Butterfly Monitoring Schemes - Italy, Portugal, Hungary, Austria, Cyprus in 2019 and Poland, Bulgaria, Malta, Czech and Croatia in 2020; seven of these have joined the eBMS data network. Further details are in Annex 2. 6. A suite of support materials has been produced, including a Butterfly Transect Manual, which has been translated into six languages and a series of regional butterfly identification guides. Videos have been made explaining how to count butterflies on a transect and PowerPoint presentations have been made available in several languages. 7. More than 20
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- 2020
14. Assessing Butterflies in Europe - Butterfly Indicators 1990-2018 Technical report
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van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C.G., Aghababyan, K., Åström, S., Balalaikins, M., Bonelli, S., Botham, M., Bourn, N., Brereton, T., Cancela, J.P., Carlisle, B., Collins, S., Dopagne, C., Dziekanska, I., Escobés, R., Faltynek Fric, Z., Feldmann, Reinart, Fernández-García, J.M., Fontaine, B., Goloshchapova, S., Gracianteparaluceta, A., Harpke, Alexander, Harrower, C., Heliölä, J., Khanamirian, G., Kolev, Z., Komac, B., Krenn, H., Kühn, Elisabeth, Lang, A., Leopold, P., Lysaght, L., Maes, D., McGowan, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Monteiro, E., Munguira, M.L., Musche, Martin, Õunap, E., Ozden, O., Paramo, F., Pavlíčko, A., Pettersson, L.B., Piqueray, J., Prokofev, I., Rákosy, L., Roth, T., Rüdisser, J., Šašić, M., Settele, Josef, Sielezniew, M., Stefanescu, C., Švitra, G., Szabadfalvi, A., Teixeira, S.M., Tiitsaar, A., Tzirkalli, E., Verovnik, R., Warren, M.S., Wynhoff, I., Roy, D.B., van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C.G., Aghababyan, K., Åström, S., Balalaikins, M., Bonelli, S., Botham, M., Bourn, N., Brereton, T., Cancela, J.P., Carlisle, B., Collins, S., Dopagne, C., Dziekanska, I., Escobés, R., Faltynek Fric, Z., Feldmann, Reinart, Fernández-García, J.M., Fontaine, B., Goloshchapova, S., Gracianteparaluceta, A., Harpke, Alexander, Harrower, C., Heliölä, J., Khanamirian, G., Kolev, Z., Komac, B., Krenn, H., Kühn, Elisabeth, Lang, A., Leopold, P., Lysaght, L., Maes, D., McGowan, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Monteiro, E., Munguira, M.L., Musche, Martin, Õunap, E., Ozden, O., Paramo, F., Pavlíčko, A., Pettersson, L.B., Piqueray, J., Prokofev, I., Rákosy, L., Roth, T., Rüdisser, J., Šašić, M., Settele, Josef, Sielezniew, M., Stefanescu, C., Švitra, G., Szabadfalvi, A., Teixeira, S.M., Tiitsaar, A., Tzirkalli, E., Verovnik, R., Warren, M.S., Wynhoff, I., and Roy, D.B.
- Abstract
There is mounting evidence of widespread declines in the diversity and abundance of insects from across the globe (Sánchez-Bayo and Wyckhuys 2019, Seibold et al. 2019, van Klink et al. 2020, Wagner 2020). This gives a stark warning for the perilous state of biodiversity (Díaz et al. 2019), and demonstrates that addressing the gap in knowledge of the status of insects is vital (Cardoso et al. 2020, Samways et al. 2020). Insects are estimated to comprise more than half of all described species and are a dominant component of biodiversity in most ecosystems (Bar-On et al. 2018). Insects also provide a crucial role in the functioning of ecosystems. They are not only related to the supply of many ecosystem services such as pollination, biological control, soil fertility regulation and diverse cultural ecosystem services but also to disservices such as damage to crops and spread of diseases to livestock and humans (Gutierrez-Arellano and Mulligan 2018, Noriega et al. 2018). There is a pressing need to assess the status of insects to set and evaluate conservation targets. At the Convention on Biological Diversity (CBD) meeting in Nagoya (Japan), the Strategic Plan for Biodiversity 2011–2020 was adopted. It proposed five goals and 20 “Aichi” biodiversity targets. In line with this plan, a new EU biodiversity strategy was adopted by the European Commission in May 2011. This strategy provided a framework for the EU to meet its biodiversity targets and global commitments as a party to the CBD. The Headline Target in the existing EU Biodiversity Strategy 2020 is to halt the loss of biodiversity and the degradation of ecosystem services in the EU by 2020, and restore them, in so far as feasible, while stepping up the EU contribution to averting global biodiversity loss. Under Target 3A the EU is committed to increasing the contribution of agriculture to biodiversity recovery. Further, the EU Biodiversity Strategy 2030 includes the development of a coherent framework for monitori
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- 2020
15. Data Integration for Large-Scale Models of Species Distributions
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Isaac, N.J.B., Jarzyna, M.A., Keil, P., Dambly, L.I., Boersch-Supan, P.H., Browning, E., Freeman, S.N., Golding, Nick, Guillera-Arroita, G., Henrys, P.A., Jarvis, S., Lahoz-Monfort, J., Pagel, J., Pescott, O.L., Schmucki, R., Simmonds, E.G., O'Hara, R.B., Isaac, N.J.B., Jarzyna, M.A., Keil, P., Dambly, L.I., Boersch-Supan, P.H., Browning, E., Freeman, S.N., Golding, Nick, Guillera-Arroita, G., Henrys, P.A., Jarvis, S., Lahoz-Monfort, J., Pagel, J., Pescott, O.L., Schmucki, R., Simmonds, E.G., and O'Hara, R.B.
- Abstract
With the expansion in the quantity and types of biodiversity data being collected, there is a need to find ways to combine these different sources to provide cohesive summaries of species’ potential and realized distributions in space and time. Recently, model-based data integration has emerged as a means to achieve this by combining datasets in ways that retain the strengths of each. We describe a flexible approach to data integration using point process models, which provide a convenient way to translate across ecological currencies. We highlight recent examples of large-scale ecological models based on data integration and outline the conceptual and technical challenges and opportunities that arise.
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- 2020
16. A new comprehensive trait database of European and Maghreb butterflies, Papilionoidea
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Middleton-Welling, J., Dapporto, L., García-Barros, E., Wiemers, Martin, Nowicki, P., Plazio, E., Bonelli, S., Zaccagno, M., Šašić, M., Liparova, J., Schweiger, Oliver, Harpke, Alexander, Musche, Martin, Settele, Josef, Schmucki, R., Shreeve, T., Middleton-Welling, J., Dapporto, L., García-Barros, E., Wiemers, Martin, Nowicki, P., Plazio, E., Bonelli, S., Zaccagno, M., Šašić, M., Liparova, J., Schweiger, Oliver, Harpke, Alexander, Musche, Martin, Settele, Josef, Schmucki, R., and Shreeve, T.
- Abstract
Trait-based analyses explaining the different responses of species and communities to environmental changes are increasing in frequency. European butterflies are an indicator group that responds rapidly to environmental changes with extensive citizen science contributions to documenting changes of abundance and distribution. Species traits have been used to explain long- and short-term responses to climate, land-use and vegetation changes. Studies are often characterised by limited trait sets being used, with risks that the relative roles of different traits are not fully explored. Butterfly trait information is dispersed amongst various sources and descriptions sometimes differ between sources. We have therefore drawn together multiple information sets to provide a comprehensive trait database covering 542 taxa and 25 traits described by 217 variables and sub-states of the butterflies of Europe and Maghreb (northwest Africa) which should serve for improved trait-based ecological, conservation-related, phylogeographic and evolutionary studies of this group of insects. We provide this data in two forms; the basic data and as processed continuous and multinomial data, to enhance its potential usage.
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- 2020
17. Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data
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Pellissier, V., primary, Schmucki, R., additional, Pe'er, G., additional, Aunins, A., additional, Brereton, T. M., additional, Brotons, L., additional, Carnicer, J., additional, Chodkiewicz, T., additional, Chylarecki, P., additional, del Moral, J. C., additional, Escandell, V., additional, Evans, D., additional, Foppen, R., additional, Harpke, A., additional, Heliölä, J., additional, Herrando, S., additional, Kuussaari, M., additional, Kühn, E., additional, Lehikoinen, A., additional, Lindström, Å., additional, Moshøj, C. M., additional, Musche, M., additional, Noble, D., additional, Oliver, T. H., additional, Reif, J., additional, Richard, D., additional, Roy, D. B., additional, Schweiger, O., additional, Settele, J., additional, Stefanescu, C., additional, Teufelbauer, N., additional, Touroult, J., additional, Trautmann, S., additional, Strien, A. J., additional, Swaay, C. A. M., additional, Turnhout, C., additional, Vermouzek, Z., additional, Voříšek, P., additional, Jiguet, F., additional, and Julliard, R., additional
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- 2020
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18. Altered parasitism of a butterfly assemblage associated with a range-expanding species
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Audusseau, H., primary, Ryrholm, N., additional, Stefanescu, C., additional, Tharel, S., additional, Jansson, C., additional, Champeaux, L., additional, Shaw, M. R., additional, Raper, C., additional, Lewis, O. T., additional, Janz, N., additional, and Schmucki, R., additional
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- 2020
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19. The EU Butterfly Indicator for Grassland species: 1990-2017. Technical report
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Van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C., Balalaikins, M., Botham, M., Bourn, N., Brereton, T., Cancela, J.P., Carlisle, B., Chambers, P., Collins, S., Dopagne, C., Escobes, R., Feldman, R., Fernandez-Garcia, J.M., Fontaine, B., Gracianteparaluceta, A., Harrower, C., Harpke, A., Heliola, J., Komac, B., Kuhn, E., Lang, A., Maes, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Munguira, M.L., Murray, T.E., Musche, M., Ounap, E., Paramo, F., Petterson, L.B., Piqueray, J., Settele, J., Stefanescu, C., Svitra, G., Tiitsaar, A., Verovnik, R., Warren, M.S., Wynhoff, I., Roy, D.B., Van Swaay, C.A.M., Dennis, E.B., Schmucki, R., Sevilleja, C., Balalaikins, M., Botham, M., Bourn, N., Brereton, T., Cancela, J.P., Carlisle, B., Chambers, P., Collins, S., Dopagne, C., Escobes, R., Feldman, R., Fernandez-Garcia, J.M., Fontaine, B., Gracianteparaluceta, A., Harrower, C., Harpke, A., Heliola, J., Komac, B., Kuhn, E., Lang, A., Maes, D., Mestdagh, X., Middlebrook, I., Monasterio, Y., Munguira, M.L., Murray, T.E., Musche, M., Ounap, E., Paramo, F., Petterson, L.B., Piqueray, J., Settele, J., Stefanescu, C., Svitra, G., Tiitsaar, A., Verovnik, R., Warren, M.S., Wynhoff, I., and Roy, D.B.
- Abstract
The EU Grassland Butterfly Indicator is one of the indicators of the status of biodiversity in the European Union. It is an abundance indicator based on data recording the population trends of seventeen butterfly species in 16 (see below) EU countries. This report presents the seventh version of this indicator now covering 28 years. At the Convention on Biological Diversity meeting in Nagoya (Japan) the Strategic Plan for Biodiversity 2011– 2020 was adopted. It proposed five goals and 20 “Aichi” biodiversity targets. In line with this plan a new EU biodiversity strategy was adopted by the European Commission in May 2011. This provided a framework for the EU to meet its own biodiversity objectives and its global commitments as a party to the CBD. The Headline Target is to halt the loss of biodiversity and the degradation of ecosystem services in the EU by 2020, and restore them, in so far as feasible, while stepping up the EU contribution to averting global biodiversity loss. Under Target 3A the EU is committed to increase the contribution of agriculture to biodiversity recovery. Europe now has one year left to intensify action to achieve this. The EU biodiversity strategy includes the development of a coherent framework for monitoring, assessing and reporting on progress in implementing actions. Such a framework is needed to link existing biodiversity data and knowledge systems with the strategy, to help assess achievement of the goals and to streamline EU and global monitoring, reporting and review obligations. Some of the EU biodiversity indicators provide specific measurements and trends on genetic, species and ecosystem/landscape diversity, but many have a more indirect link to biodiversity. Very few have been established specifically to assess biodiversity. The status indicators on species only cover birds, bats and butterflies, since these are the only taxa/species groups for which harmonized European monitoring data are available (EEA, 2012). For the EU Grass
- Published
- 2019
20. The National Plant Monitoring Scheme: a technical review
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Pescott, O.L., Walker, K.J., Jitlal, M., Smart, S.M., Maskell, L., Schmucki, R., Day, J., Amos, C., Peck, K., Robinson, A., Roy, D.B., Pescott, O.L., Walker, K.J., Jitlal, M., Smart, S.M., Maskell, L., Schmucki, R., Day, J., Amos, C., Peck, K., Robinson, A., and Roy, D.B.
- Abstract
The National Plant Monitoring Scheme, coordinated by the Botanical Society of Britain and Ireland, the Centre for Ecology & Hydrology, JNCC and Plantlife, was launched in 2015 to provide an indication of the status and trends of plants and semi-natural habitats across the UK. The scheme is based on volunteer recording according to a set protocol at pre-determined monads selected through a weighted-random sampling scheme.
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- 2019
21. Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data
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Pellissier, V., Schmucki, R., Pe'er, Guy, Aunins, A., Brereton, T.M., Brotons, L., Carnicer, J., Chodkiewicz, T., Chylarecki, P., del Moral, J.C., Escandell, V., Evans, D., Foppen, R., Harpke, Alexander, Heliölä, J., Herrando, S., Kuussaari, M., Kühn, Elisabeth, Lehikoinen, A., Lindström, Å., Moshøj, C.M., Musche, Martin, Noble, D., Oliver, T.H., Reif, J., Richard, D., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., Teufelbauer, N., Touroult, J., Trautmann, S., van Strien, A.J., van Swaay, C.A.M., Van Turnhout, C., Vermouzek, Z., Voříšek, P., Jiguet, F., Julliard, R., Pellissier, V., Schmucki, R., Pe'er, Guy, Aunins, A., Brereton, T.M., Brotons, L., Carnicer, J., Chodkiewicz, T., Chylarecki, P., del Moral, J.C., Escandell, V., Evans, D., Foppen, R., Harpke, Alexander, Heliölä, J., Herrando, S., Kuussaari, M., Kühn, Elisabeth, Lehikoinen, A., Lindström, Å., Moshøj, C.M., Musche, Martin, Noble, D., Oliver, T.H., Reif, J., Richard, D., Roy, D.B., Schweiger, Oliver, Settele, Josef, Stefanescu, C., Teufelbauer, N., Touroult, J., Trautmann, S., van Strien, A.J., van Swaay, C.A.M., Van Turnhout, C., Vermouzek, Z., Voříšek, P., Jiguet, F., and Julliard, R.
- Abstract
The European Union's Natura 2000 (N2000) is among the largest international networks of protected areas. One of its aims is to secure the status of a predetermined set of (targeted) bird and butterfly species. However, nontarget species may also benefit from N2000. We evaluated how the terrestrial component of this network affects the abundance of nontargeted, more common bird and butterfly species based on data from long‐term volunteer‐based monitoring programs in 9602 sites for birds and 2001 sites for butterflies. In almost half of the 155 bird species assessed, and particularly among woodland specialists, abundance increased (slope estimates ranged from 0.101 [SD 0.042] to 3.51 [SD 1.30]) as the proportion of landscape covered by N2000 sites increased. This positive relationship existed for 27 of the 104 butterfly species (estimates ranged from 0.382 [SD 0.163] to 4.28 [SD 0.768]), although most butterflies were generalists. For most species, when land‐cover covariates were accounted for these positive relationships were not evident, meaning land cover may be a determinant of positive effects of the N2000 network. The increase in abundance as N2000 coverage increased correlated with the specialization index for birds, but not for butterflies. Although the N2000 network supports high abundance of a large spectrum of species, the low number of specialist butterflies with a positive association with the N2000 network shows the need to improve the habitat quality of N2000 sites that could harbor open‐land butterfly specialists. For a better understanding of the processes involved, we advocate for standardized collection of data at N2000 sites.
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- 2019
22. European butterfly populations vary in sensitivity to weather across their geographical ranges
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Mills, S.C., Oliver, T.H., Bradbury, R.B., Gregory, R.D., Brereton, T., Kühn, E., Kuussaari, M., Musche, M., Roy, D.B., Schmucki, R., Stefanescu, C., van Swaay, C., and Evans, K.L.
- Abstract
Aim: The aim was to assess the sensitivity of butterfly population dynamics to variation in weather conditions across their geographical ranges, relative to sensitivity to density dependence, and determine whether sensitivity is greater towards latitudinal range margins. Location: Europe. Time period: 1980–2014. Major taxa studied: Butterflies. Methods: We use long-term (35 years) butterfly monitoring data from > 900 sites, ranging from Finland to Spain, grouping sites into 2° latitudinal bands. For 12 univoltine butterfly species with sufficient data from at least four bands, we construct population growth rate models that include density dependence, temperature and precipitation during distinct life-cycle periods, defined to accommodate regional variation in phenology. We use partial R 2 values as indicators of butterfly population dynamics' sensitivity to weather and density dependence, and assess how these vary with latitudinal position within a species' distribution. Results: Population growth rates appear uniformly sensitive to density dependence across species' geographical distributions, and sensitivity to density dependence is typically greater than sensitivity to weather. Sensitivity to weather is greatest towards range edges, with symmetry in northern and southern parts of the range. This pattern is not driven by variation in the magnitude of weather variability across the range, topographic heterogeneity, latitudinal range extent or phylogeny. Significant weather variables in population growth rate models appear evenly distributed across the life cycle and across temperature and precipitation, with substantial intraspecific variation across the geographical ranges in the associations between population dynamics and specific weather variables. Main conclusions: Range-edge populations appear more sensitive to changes in weather than those nearer the centre of species' distributions, but density dependence does not exhibit this pattern. Precipitation is as important as temperature in driving butterfly population dynamics. Intraspecific variation in the form and strength of sensitivity to weather suggests that there may be important geographical variation in populations' responses to climate change.
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- 2017
23. NMR solution structure of the TSL2 RNA hairpin
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Garcia-Lopez, A., primary, Wacker, A., additional, Tessaro, F., additional, Jonker, H.R.A., additional, Richter, C., additional, Comte, A., additional, Berntenis, N., additional, Schmucki, R., additional, Hatje, K., additional, Sciarra, D., additional, Konieczny, P., additional, Fournet, G., additional, Faustino, I., additional, Orozco, M., additional, Artero, R., additional, Goekjian, P., additional, Metzger, F., additional, Ebeling, M., additional, Joseph, B., additional, Schwalbe, H., additional, and Scapozza, L., additional
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- 2018
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24. Technical report: making Bioscore distribution models based on Butterfly Monitoring Transects
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van Swaay, C.A.M., Botham, M., Brereton, T., Carlisle, B., Dopagne, C., Escobés, R., Feldmann, Reinart, Fernández-García, J.M., Fontaine, B., Gracianteparaluceta, A., Harpke, Alexander, Heliölä, J., Kühn, Elisabeth, Lang, A., Maes, D., Mestdagh, X., Monasterio, Y., Munguira, M.L., Murray, T., Musche, Martin, Õunap, E., Pettersson, L.B., Piqueray, J., Roth, T., Roy, D.B., Schmucki, R., Settele, Josef, Stefanescu, C., Švitra, G., Tiitsaar, A., Verovnik, R., van Swaay, C.A.M., Botham, M., Brereton, T., Carlisle, B., Dopagne, C., Escobés, R., Feldmann, Reinart, Fernández-García, J.M., Fontaine, B., Gracianteparaluceta, A., Harpke, Alexander, Heliölä, J., Kühn, Elisabeth, Lang, A., Maes, D., Mestdagh, X., Monasterio, Y., Munguira, M.L., Murray, T., Musche, Martin, Õunap, E., Pettersson, L.B., Piqueray, J., Roth, T., Roy, D.B., Schmucki, R., Settele, Josef, Stefanescu, C., Švitra, G., Tiitsaar, A., and Verovnik, R.
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- 2017
25. Binding to a novel RNA-protein complex creates specificity for small molecule splicing modifiers to treat SMA
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Sivaramakrishnan, M., primary, McCarthy, K.D., additional, Huber, S., additional, Campagne, S., additional, Meier, S., additional, Augustin, A., additional, Heckel, T., additional, Meistermann, H., additional, Hug, M., additional, Birrer, P., additional, Moursy, A., additional, Khawaja, S., additional, Schmucki, R., additional, Berntenis, N., additional, Giroud, N., additional, Golling, S., additional, Tzouros, M., additional, Banfai, B., additional, Duran-Pacheco, G., additional, Lamerz, J., additional, Liu, Y.H., additional, Luebbers, T., additional, Ratni, H., additional, Clery, A., additional, Ebeling, M., additional, Paushkin, S., additional, Krainer, A.R., additional, Allain, F., additional, and Metzger, F., additional
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- 2017
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26. A regionally informed abundance index for supporting integrative analyses across butterfly monitoring schemes
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Schmucki, R., Pe'er, Guy, Roy, D.B., Stefanescu, C., van Swaay, C.A.M., Oliver, T.H., Kuussaari, M., van Strien, A.J., Ries, L., Settele, Josef, Musche, Martin, Carnicer, J., Schweiger, Oliver, Brereton, T., Harpke, Alexander, Heliölä, J., Kühn, Elisabeth, Julliard, R., Schmucki, R., Pe'er, Guy, Roy, D.B., Stefanescu, C., van Swaay, C.A.M., Oliver, T.H., Kuussaari, M., van Strien, A.J., Ries, L., Settele, Josef, Musche, Martin, Carnicer, J., Schweiger, Oliver, Brereton, T., Harpke, Alexander, Heliölä, J., Kühn, Elisabeth, and Julliard, R.
- Abstract
1.The rapid expansion of systematic monitoring schemes necessitates robust methods to reliably assess species’ status and trends. Insect monitoring poses a challenge where there are strong seasonal patterns, requiring repeated counts to reliably assess abundance. Butterfly Monitoring Schemes (BMSs) operate in an increasing number of countries with broadly the same methodology, yet they differ in their observation frequency and in the methods used to compute annual abundance indices.2.Using simulated and observed data, we performed an extensive comparison of two approaches used to derive abundance indices from count data collected via BMS, under a range of sampling frequencies. Linear interpolation is most commonly used to estimate abundance indices from seasonal count series. A second method, hereafter the regional GAM, fits a generalized additive model to repeated counts within sites across a climatic region. For the two methods we estimated bias in abundance indices and the statistical power for detecting trends given different proportions of missing counts. We also compared the accuracy of trend estimates using systematically degraded observed counts of the Gatekeeper Pyronia tithonus (Linnaeus 1767).3.The regional GAM method generally outperforms the linear interpolation method. When the proportion of missing counts increased beyond 50%, indices derived via the linear interpolation method showed substantially higher estimation error as well as clear biases, in comparison to the regional GAM method. The regional GAM method also showed higher power to detect trends when the proportion of missing counts was substantial.4.Synthesis and applications. Monitoring offers invaluable data to support conservation policy and management, but requires robust analysis approaches and guidance for new and expanding schemes. Based on our findings, we recommend the regional generalized additive model approach when conducting integrative analyses across schemes, or when analysing s
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- 2015
27. Jahresauswertung 2012 des Tagfalter-Monitoring Deutschland
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Kühn, Elisabeth, Musche, Martin, Harpke, Alexander, Schmucki, R., Feldmann, Reinart, Wiemers, Martin, Hirneisen, N., Settele, Josef, Kühn, Elisabeth, Musche, Martin, Harpke, Alexander, Schmucki, R., Feldmann, Reinart, Wiemers, Martin, Hirneisen, N., and Settele, Josef
- Abstract
no abstract
- Published
- 2014
28. MN14 - Binding to a novel RNA-protein complex creates specificity for small molecule splicing modifiers to treat SMA
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Sivaramakrishnan, M., McCarthy, K.D., Huber, S., Campagne, S., Meier, S., Augustin, A., Heckel, T., Meistermann, H., Hug, M., Birrer, P., Moursy, A., Khawaja, S., Schmucki, R., Berntenis, N., Giroud, N., Golling, S., Tzouros, M., Banfai, B., Duran-Pacheco, G., Lamerz, J., Liu, Y.H., Luebbers, T., Ratni, H., Clery, A., Ebeling, M., Paushkin, S., Krainer, A.R., Allain, F., and Metzger, F.
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- 2017
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29. Solution structure of Polytheonamide B
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Hamada, N., primary, Matsunaga, S., additional, Fujiwara, M., additional, Fujjita, K., additional, Hirota, H., additional, Schmucki, R., additional, Guntert, P., additional, and Fusetani, N., additional
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- 2010
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30. Solution structure of the beta-E-domain of wheat Ec-1 metallothionein
- Author
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Peroza, E.A., primary, Schmucki, R., additional, Guntert, P., additional, Freisinger, E., additional, and Zerbe, O., additional
- Published
- 2009
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31. splicekit : an integrative toolkit for splicing analysis from short-read RNA-seq.
- Author
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Rot G, Wehling A, Schmucki R, Berntenis N, Zhang JD, and Ebeling M
- Abstract
Motivation: Analysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. To the best of our knowledge, there is currently no integrative open-source software dedicated to this task., Results: Here, we introduce splicekit , a Python package that provides and integrates a set of existing and novel splicing analysis tools for conducting splicing analysis., Availability and Implementation: The software splicekit is open-source and available at Github (https://github.com/bedapub/splicekit) and via the Python Package Index., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press.)
- Published
- 2024
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32. Mechanisms underpinning community stability along a latitudinal gradient: Insights from a niche-based approach.
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Evans LC, Melero Y, Schmucki R, Boersch-Supan PH, Brotons L, Fontaine C, Jiguet F, Kuussaari M, Massimino D, Robinson RA, Roy DB, Schweiger O, Settele J, Stefanescu C, van Turnhout CAM, and Oliver TH
- Subjects
- Animals, Biodiversity, Bayes Theorem, Europe, Ecosystem, Butterflies
- Abstract
At large scales, the mechanisms underpinning stability in natural communities may vary in importance due to changes in species composition, mean abundance, and species richness. Here we link species characteristics (niche positions) and community characteristics (richness and abundance) to evaluate the importance of stability mechanisms in 156 butterfly communities monitored across three European countries and spanning five bioclimatic regions. We construct niche-based hierarchical structural Bayesian models to explain first differences in abundance, population stability, and species richness between the countries, and then explore how these factors impact community stability both directly and indirectly (via synchrony and population stability). Species richness was partially explained by the position of a site relative to the niches of the species pool, and species near the centre of their niche had higher average population stability. The differences in mean abundance, population stability, and species richness then influenced how much variation in community stability they explained across the countries. We found, using variance partitioning, that community stability in Finnish communities was most influenced by community abundance, whereas this aspect was unimportant in Spain with species synchrony explaining most variation; the UK was somewhat intermediate with both factors explaining variation. Across all countries, the diversity-stability relationship was indirect with species richness reducing synchrony which increased community stability, with no direct effects of species richness. Our results suggest that in natural communities, biogeographical variation observed in key drivers of stability, such as population abundance and species richness, leads to community stability being limited by different factors and that this can partially be explained due to the niche characteristics of the European butterfly assemblage., (© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)
- Published
- 2023
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33. A humanized minipig model for the toxicological testing of therapeutic recombinant antibodies.
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Flisikowska T, Egli J, Flisikowski K, Stumbaum M, Küng E, Ebeling M, Schmucki R, Georges G, Singer T, Kurome M, Kessler B, Zakhartchenko V, Wolf E, Weber F, Schnieke A, and Iglesias A
- Subjects
- Mice, Humans, Animals, Swine, Swine, Miniature, Recombinant Proteins, Mice, Transgenic, Immunoglobulin Heavy Chains genetics
- Abstract
The safety of most human recombinant proteins can be evaluated in transgenic mice tolerant to specific human proteins. However, owing to insufficient genetic diversity and to fundamental differences in immune mechanisms, small-animal models of human diseases are often unsuitable for immunogenicity testing and for predicting adverse outcomes in human patients. Most human therapeutic antibodies trigger xenogeneic responses in wild-type animals and thus rapid clearance of the drugs, which makes in vivo toxicological testing of human antibodies challenging. Here we report the generation of Göttingen minipigs carrying a mini-repertoire of human genes for the immunoglobulin heavy chains γ1 and γ4 and the immunoglobulin light chain κ. In line with observations in human patients, the genetically modified minipigs tolerated the clinically non-immunogenic IgG1κ-isotype monoclonal antibodies daratumumab and bevacizumab, and elicited antibodies against the checkpoint inhibitor atezolizumab and the engineered interleukin cergutuzumab amunaleukin. The humanized minipigs can facilitate the safety and efficacy testing of therapeutic antibodies., (© 2022. The Author(s).)
- Published
- 2022
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34. Helicopter inter-hospital transfer for patients undergoing extracorporeal membrane oxygenation: a retrospective 12-year analysis of a service system.
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Fuchs A, Schmucki R, Meuli L, Wendel-Garcia PD, Albrecht R, Greif R, and Pietsch U
- Subjects
- Aircraft, Critical Illness, Female, Hospitals, Humans, Male, Middle Aged, Patient Transfer methods, Retrospective Studies, Extracorporeal Membrane Oxygenation methods
- Abstract
Background: Patients undergoing extracorporeal membrane oxygenation (ECMO) are critically ill and show high mortality. Inter-hospital transfer of these patients has to be safe, with high survival rates during transport without potentially serious and life-threatening adverse events. The Swiss Air-Rescue provides 24-h/7-days per week inter-hospital helicopter transfers that include on-site ECMO cannulation if needed. This retrospective observational study describes adverse events of patients on ECMO transported by helicopter, and their associated survival., Methods: All patients on ECMO with inter-hospital transfer by helicopter from start of service in February 2009 until May 2021 were included. Patients not transported by helicopter or with missing medical records were excluded. Patient demographics (age, sex) and medical history (type of and reason for ECMO), mission details (flight distance, times, primary or secondary transport), adverse events during the inter-hospital transfer, and survival of transferred patients were recorded. The primary endpoint was patient survival during transfer. Secondary endpoints were adverse events during transfer and 28-day survival., Results: We screened 214 ECMO-related missions and included 191 in this analysis. Median age was 54.6 [IQR 46.1-62.0] years, 70.7% were male, and most patients had veno-arterial ECMO (56.5%). The main reasons for ECMO were pulmonary (46.1%) or cardiac (44.0%) failure. Most were daytime (69.8%) and primary missions (n = 100), median total mission time was 182.0 [143.0-254.0] min, and median transfer distance was 52.7 [33.2-71.1] km. All patients survived the transfer. Forty-four adverse events were recorded during 37 missions (19.4%), where 31 (70.5%) were medical and none resulted in patient harm. Adverse events occurred more frequently during night-time missions (59.9%, p = 0.047). Data for 28-day survival were available for 157 patients, of which 86 (54.8%) were alive., Conclusion: All patients under ECMO survived the helicopter transport. Adverse events were observed for about 20% of the flight missions, with a tendency during the night-time flights, none harmed the patients. Inter-hospital transfer for patients undergoing ECMO provided by 24-h/7-d per week helicopter emergency medical service teams can be considered as feasible and safe. The majority of the patients (54.8%) were still alive after 28 days., (© 2022. The Author(s).)
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- 2022
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35. Local adaptation to climate anomalies relates to species phylogeny.
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Melero Y, Evans LC, Kuussaari M, Schmucki R, Stefanescu C, Roy DB, and Oliver TH
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- Animal Distribution, Animals, Computer Simulation, Europe, Phylogeography, Adaptation, Physiological genetics, Butterflies genetics, Butterflies physiology, Climate, Ecosystem, Phylogeny
- Abstract
Climatic anomalies are increasing in intensity and frequency due to rapid rates of global change, leading to increased extinction risk for many species. The impacts of anomalies are likely to vary between species due to different degrees of sensitivity and extents of local adaptation. Here, we used long-term butterfly monitoring data of 143 species across six European bioclimatic regions to show how species' population dynamics have responded to local or globally-calculated climatic anomalies, and how species attributes mediate these responses. Contrary to expectations, degree of apparent local adaptation, estimated from the relative population sensitivity to local versus global anomalies, showed no associations with species mobility or reproductive rate but did contain a strong phylogenetic signal. The existence of phylogenetically-patterned local adaptation to climate has important implications for forecasting species responses to current and future climatic conditions and for developing appropriate conservation practices., (© 2022. The Author(s).)
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- 2022
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36. Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research.
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Mädler SC, Julien-Laferriere A, Wyss L, Phan M, Sonrel A, Kang ASW, Ulrich E, Schmucki R, Zhang JD, Ebeling M, Badi L, Kam-Thong T, Schwalie PC, and Hatje K
- Abstract
Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of disease biology. The promise it presents to also transform translational research requires highly standardized and robust software workflows. Here, we present the toolkit Besca , which streamlines scRNA-seq analyses and their use to deconvolute bulk RNA-seq data according to current best practices. Beyond a standard workflow covering quality control, filtering, and clustering, two complementary Besca modules, utilizing hierarchical cell signatures and supervised machine learning, automate cell annotation and provide harmonized nomenclatures. Subsequently, the gene expression profiles can be employed to estimate cell type proportions in bulk transcriptomics data. Using multiple, diverse scRNA-seq datasets, some stemming from highly heterogeneous tumor tissue, we show how Besca aids acceleration, interoperability, reusability and interpretability of scRNA-seq data analyses, meeting crucial demands in translational research and beyond., (© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
- Published
- 2021
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37. Sodium Iodate-Induced Degeneration Results in Local Complement Changes and Inflammatory Processes in Murine Retina.
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Enzbrenner A, Zulliger R, Biber J, Pousa AMQ, Schäfer N, Stucki C, Giroud N, Berrera M, Kortvely E, Schmucki R, Badi L, Grosche A, Pauly D, and Enzmann V
- Subjects
- Animals, Apoptosis genetics, Apoptosis immunology, Complement System Proteins genetics, Disease Models, Animal, Fluorescent Antibody Technique, Gene Expression Regulation drug effects, Immunity, Innate, Immunohistochemistry, Mice, Retinal Degeneration pathology, Complement System Proteins immunology, Complement System Proteins metabolism, Disease Susceptibility, Iodates adverse effects, Retinal Degeneration etiology, Retinal Degeneration metabolism
- Abstract
Age-related macular degeneration (AMD), one of the leading causes of blindness worldwide, causes personal suffering and high socioeconomic costs. While there has been progress in the treatments for the neovascular form of AMD, no therapy is yet available for the more common dry form, also known as geographic atrophy. We analysed the retinal tissue in a mouse model of retinal degeneration caused by sodium iodate (NaIO
3 )-induced retinal pigment epithelium (RPE) atrophy to understand the underlying pathology. RNA sequencing (RNA-seq), qRT-PCR, Western blot, immunohistochemistry of the retinas and multiplex ELISA of the mouse serum were applied to find the pathways involved in the degeneration. NaIO3 caused patchy RPE loss and thinning of the photoreceptor layer. This was accompanied by the increased retinal expression of complement components c1s, c3 , c4 , cfb and cfh . C1s, C3, CFH and CFB were complement proteins, with enhanced deposition at day 3. C4 was upregulated in retinal degeneration at day 10. Consistently, the transcript levels of proinflammatory ccl-2 , -3 , -5 , il-1β , il-33 and tgf-β were increased in the retinas of NaIO3 mice, but vegf-a mRNA was reduced. Macrophages, microglia and gliotic Müller cells could be a cellular source for local retinal inflammatory changes in the NaIO3 retina. Systemic complement and cytokines/chemokines remained unaltered in this model of NaIO3 -dependent retinal degeneration. In conclusion, systemically administered NaIO3 promotes degenerative and inflammatory processes in the retina, which can mimic the hallmarks of geographic atrophy.- Published
- 2021
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38. Inferring species interactions from ecological survey data: A mechanistic approach to predict quantitative food webs of seed feeding by carabid beetles.
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Pocock MJO, Schmucki R, and Bohan DA
- Abstract
Ecological networks are valuable for ecosystem analysis but their use is often limited by a lack of data because many types of ecological interaction, for example, predation, are short-lived and difficult to observe or detect. While there are different methods for inferring the presence of interactions, they have rarely been used to predict the interaction strengths that are required to construct weighted, or quantitative, ecological networks.Here, we develop a trait-based approach suitable for inferring weighted networks, that is, with varying interaction strengths. We developed the method for seed-feeding carabid ground beetles (Coleoptera: Carabidae) although the principles can be applied to other species and types of interaction.Using existing literature data from experimental seed-feeding trials, we predicted a per-individual interaction cost index based on carabid and seed size. This was scaled up to the population level to create inferred weighted networks using the abundance of carabids and seeds from empirical samples and energetic intake rates of carabids from the literature. From these weighted networks, we also derived a novel measure of expected predation pressure per seed type per network.This method was applied to existing ecological survey data from 255 arable fields with carabid data from pitfall traps and plant seeds from seed rain traps. Analysis of these inferred networks led to testable hypotheses about how network structure and predation pressure varied among fields.Inferred networks are valuable because (a) they provide null models for the structuring of food webs to test against empirical species interaction data, for example, DNA analysis of carabid gut regurgitates and (b) they allow weighted networks to be constructed whenever we can estimate interactions between species and have ecological census data available. This permits ecological network analysis even at times and in places when interactions were not directly assessed., Competing Interests: The authors declare no conflicts of interest., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
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- 2021
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39. Combining range and phenology shifts offers a winning strategy for boreal Lepidoptera.
- Author
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Hällfors MH, Pöyry J, Heliölä J, Kohonen I, Kuussaari M, Leinonen R, Schmucki R, Sihvonen P, and Saastamoinen M
- Subjects
- Animals, Climate Change, Seasons, Temperature, Lepidoptera
- Abstract
Species can adapt to climate change by adjusting in situ or by dispersing to new areas, and these strategies may complement or enhance each other. Here, we investigate temporal shifts in phenology and spatial shifts in northern range boundaries for 289 Lepidoptera species by using long-term data sampled over two decades. While 40% of the species neither advanced phenology nor moved northward, nearly half (45%) used one of the two strategies. The strongest positive population trends were observed for the minority of species (15%) that both advanced flight phenology and shifted their northern range boundaries northward. We show that, for boreal Lepidoptera, a combination of phenology and range shifts is the most viable strategy under a changing climate. Effectively, this may divide species into winners and losers based on their propensity to capitalize on this combination, with potentially large consequences on future community composition., (© 2021 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)
- Published
- 2021
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40. CD22 Blockage Restores Age-Related Impairments of Microglia Surveillance Capacity.
- Author
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Aires V, Coulon-Bainier C, Pavlovic A, Ebeling M, Schmucki R, Schweitzer C, Kueng E, Gutbier S, and Harde E
- Subjects
- Aging drug effects, Aging genetics, Animals, Brain drug effects, Brain physiology, Cell Count, Disease Models, Animal, Humans, Macrophages metabolism, Male, Mice, Microglia cytology, Phagocytosis genetics, Sialic Acid Binding Ig-like Lectin 2 genetics, Sialic Acid Binding Ig-like Lectin 2 metabolism, Signal Transduction, Aging physiology, Brain cytology, Microglia drug effects, Phagocytosis drug effects, Sialic Acid Binding Ig-like Lectin 2 antagonists & inhibitors
- Abstract
Microglia, the innate immune cells of the brain, are essential for maintaining homeostasis by their ramified, highly motile processes and for orchestrating the immune response to pathological stimuli. They are implicated in several neurodegenerative diseases like Alzheimer's and Parkinson's disease. One commonality of these diseases is their strong correlation with aging as the highest risk factor and studying age-related alterations in microglia physiology and associated signaling mechanism is indispensable for a better understanding of age-related pathomechanisms. CD22 has been identified as a modifier of microglia phagocytosis in a recent study, but not much is known about the function of CD22 in microglia. Here we show that CD22 surface levels are upregulated in aged versus adult microglia. Furthermore, in the amyloid mouse model PS2APP, Aβ-containing microglia also exhibit increased CD22 signal. To assess the impact of CD22 blockage on microglia morphology and dynamics, we have established a protocol to image microglia process motility in acutely prepared brain slices from CX3CR1-GFP reporter mice. We observed a significant reduction of microglial ramification and surveillance capacity in brain slices from aged versus adult mice. The age-related decrease in surveillance can be restored by antibody-mediated CD22 blockage in aged mice, whereas surveillance in adult mice is not affected by CD22 inhibition. Moreover to complement the results obtained in mice, we show that human iPSC-derived macrophages exhibit an increased phagocytic capacity upon CD22 blockage. Downstream analysis of antibody-mediated CD22 inhibition revealed an influence on BMP and TGFβ associated gene networks. Our results demonstrate CD22 as a broad age-associated modulator of microglia functionality with potential implications for neurodegenerative disorders., Competing Interests: During the course of this study, all authors are or were full time employees or trainees at Roche and they may additionally hold Roche stock/stock options. The reviewer DE declared a shared affiliation with one of the authors VA to the handling editor at the time of the review., (Copyright © 2021 Aires, Coulon-Bainier, Pavlovic, Ebeling, Schmucki, Schweitzer, Kueng, Gutbier and Harde.)
- Published
- 2021
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41. Identification of Natural Antisense Transcripts in Mouse Brain and Their Association With Autism Spectrum Disorder Risk Genes.
- Author
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Koç B, Fucile G, Schmucki R, Giroud N, Bergauer T, and Hall BJ
- Abstract
Genome-wide sequencing technologies have greatly contributed to our understanding of the genetic basis of neurodevelopmental disorders such as autism spectrum disorder (ASD). Interestingly, a number of ASD-related genes express natural antisense transcripts (NATs). In some cases, these NATs have been shown to play a regulatory role in sense strand gene expression and thus contribute to brain function. However, a detailed study examining the transcriptional relationship between ASD-related genes and their NAT partners is lacking. We performed strand-specific, deep RNA sequencing to profile expression of sense and antisense reads with a focus on 100 ASD-related genes in medial prefrontal cortex (mPFC) and striatum across mouse post-natal development (P7, P14, and P56). Using de novo transcriptome assembly, we generated a comprehensive long non-coding RNA (lncRNA) transcriptome. We conducted BLAST analyses to compare the resultant transcripts with the human genome and identified transcripts with high sequence similarity and coverage. We assembled 32861 de novo antisense transcripts mapped to 12182 genes, of which 1018 are annotated by Ensembl as lncRNA. We validated the expression of a subset of selected ASD-related transcripts by PCR, including Syngap1 and Cntnap2 . Our analyses revealed that more than 70% (72/100) of the examined ASD-related genes have one or more expressed antisense transcripts, suggesting more ASD-related genes than previously thought could be subject to NAT-mediated regulation in mice. We found that expression levels of antisense contigs were mostly positively correlated with their cognate coding sense strand RNA transcripts across developmental age. A small fraction of the examined transcripts showed brain region specific enrichment, indicating possible circuit-specific roles. Our BLAST analyses identified 110 of 271 ASD-related de novo transcripts with >90% identity to the human genome at >90% coverage. These findings, which include an assembled de novo antisense transcriptome, contribute to the understanding of NAT regulation of ASD-related genes in mice and can guide NAT-mediated gene regulation strategies in preclinical investigations toward the ultimate goal of developing novel therapeutic targets for ASD., Competing Interests: BK, RS, NG, TB, and BJH were full time employees of F. Hoffmann-La Roche Ltd. of Basel, Switzerland during the course of studies. The remaining author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Koç, Fucile, Schmucki, Giroud, Bergauer and Hall.)
- Published
- 2021
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42. Enriching the Shared Socioeconomic Pathways to co-create consistent multi-sector scenarios for the UK.
- Author
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Pedde S, Harrison PA, Holman IP, Powney GD, Lofts S, Schmucki R, Gramberger M, and Bullock JM
- Abstract
As the pressure to take action against global warming is growing in urgency, scenarios that incorporate multiple social, economic and environmental drivers become increasingly critical to support governments and other stakeholders in planning climate change mitigation or adaptation actions. This has led to the recent explosion of future scenario analyses at multiple scales, further accelerated since the development of the Intergovernmental Panel on Climate Change (IPCC) research community Shared Socioeconomic Pathways (SSPs) and Representative Concentration Pathways (RCPs). While RCPs have been widely applied to climate models to produce climate scenarios at multiple scales for investigating climate change impacts, adaptation and vulnerabilities (CCIAV), SSPs are only recently being scaled for different geographical and sectoral applications. This is seen in the UK where significant investment has produced the RCP-based UK Climate Projections (UKCP18), but no equivalent UK version of the SSPs exists. We address this need by developing a set of multi-driver qualitative and quantitative UK-SSPs, following a state-of-the-art scenario methodology that integrates national stakeholder knowledge on locally-relevant drivers and indicators with higher level information from European and global SSPs. This was achieved through an intensive participatory process that facilitated the combination of bottom-up and top-down approaches to develop a set of UK-specific SSPs that are locally comprehensive, yet consistent with the global and European SSPs. The resulting scenarios balance the importance of consistency and legitimacy, demonstrating that divergence is not necessarily the result of inconsistency, nor comes as a choice to contextualise narratives at the appropriate scale., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)
- Published
- 2021
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43. Alzheimer's Risk Gene TREM2 Determines Functional Properties of New Type of Human iPSC-Derived Microglia.
- Author
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Reich M, Paris I, Ebeling M, Dahm N, Schweitzer C, Reinhardt D, Schmucki R, Prasad M, Köchl F, Leist M, Cowley SA, Zhang JD, Patsch C, Gutbier S, and Britschgi M
- Subjects
- Cell Differentiation, Cells, Cultured, Genetic Predisposition to Disease, Humans, Membrane Glycoproteins genetics, Receptors, Immunologic genetics, Alzheimer Disease, Cell Culture Techniques methods, Induced Pluripotent Stem Cells metabolism, Membrane Glycoproteins metabolism, Microglia metabolism, Receptors, Immunologic metabolism
- Abstract
Microglia are key in the homeostatic well-being of the brain and microglial dysfunction has been implicated in neurodegenerative disorders such as Alzheimer's disease (AD). Due to the many limitations to study microglia in situ or isolated for large scale drug discovery applications, there is a high need to develop robust and scalable human cellular models of microglia with reliable translatability to the disease. Here, we describe the generation of microglia-like cells from human induced pluripotent stem cells (iPSC) with distinct phenotypes for mechanistic studies in AD. We started out from an established differentiation protocol to generate primitive macrophage precursors mimicking the yolk sac ontogeny of microglia. Subsequently, we tested 36 differentiation conditions for the cells in monoculture where we exposed them to various combinations of media, morphogens, and extracellular matrices. The optimized protocol generated robustly ramified cells expressing key microglial markers. Bulk mRNA sequencing expression profiles revealed that compared to cells obtained in co-culture with neurons, microglia-like cells derived from a monoculture condition upregulate mRNA levels for Triggering Receptor Expressed On Myeloid Cells 2 (TREM2), which is reminiscent to the previously described disease-associated microglia. TREM2 is a risk gene for AD and an important regulator of microglia. The regulatory function of TREM2 in these cells was confirmed by comparing wild type with isogenic TREM2 knock-out iPSC microglia. The TREM2-deficient cells presented with stronger increase in free cytosolic calcium upon stimulation with ATP and ADP, as well as stronger migration towards complement C5a, compared to TREM2 expressing cells. The functional differences were associated with gene expression modulation of key regulators of microglia. In conclusion, we have established and validated a work stream to generate functional human iPSC-derived microglia-like cells by applying a directed and neuronal co-culture independent differentiation towards functional phenotypes in the context of AD. These cells can now be applied to study AD-related disease settings and to perform compound screening and testing for drug discovery., Competing Interests: During the course of this study, MR, IP, ND, CS, DR, RS, ME, JZ, CP, SG, and MB are or were full time employees or trainees at Roche and they may additionally hold Roche stock/stock options. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Reich, Paris, Ebeling, Dahm, Schweitzer, Reinhardt, Schmucki, Prasad, Köchl, Leist, Cowley, Zhang, Patsch, Gutbier and Britschgi.)
- Published
- 2021
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44. A new comprehensive trait database of European and Maghreb butterflies, Papilionoidea.
- Author
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Middleton-Welling J, Dapporto L, García-Barros E, Wiemers M, Nowicki P, Plazio E, Bonelli S, Zaccagno M, Šašić M, Liparova J, Schweiger O, Harpke A, Musche M, Settele J, Schmucki R, and Shreeve T
- Subjects
- Africa, Northern, Animals, Biological Evolution, Conservation of Natural Resources, Databases, Factual, Ecology, Europe, Phylogeny, Butterflies classification
- Abstract
Trait-based analyses explaining the different responses of species and communities to environmental changes are increasing in frequency. European butterflies are an indicator group that responds rapidly to environmental changes with extensive citizen science contributions to documenting changes of abundance and distribution. Species traits have been used to explain long- and short-term responses to climate, land-use and vegetation changes. Studies are often characterised by limited trait sets being used, with risks that the relative roles of different traits are not fully explored. Butterfly trait information is dispersed amongst various sources and descriptions sometimes differ between sources. We have therefore drawn together multiple information sets to provide a comprehensive trait database covering 542 taxa and 25 traits described by 217 variables and sub-states of the butterflies of Europe and Maghreb (northwest Africa) which should serve for improved trait-based ecological, conservation-related, phylogeographic and evolutionary studies of this group of insects. We provide this data in two forms; the basic data and as processed continuous and multinomial data, to enhance its potential usage.
- Published
- 2020
- Full Text
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45. Ecology and Genetic Structure of the Parasitoid Phobocampe confusa (Hymenoptera: Ichneumonidae) in Relation to Its Hosts, Aglais Species (Lepidoptera: Nymphalidae).
- Author
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Audusseau H, Baudrin G, Shaw MR, Keehnen NLP, Schmucki R, and Dupont L
- Abstract
The biology of parasitoids in natural ecosystems remains very poorly studied, though they are key species for their functioning. Here we focused on Phobocampe confusa , a Nymphalini specialist, responsible for high mortality rates in charismatic butterfly species in Europe (genus Aglais ). We studied its ecology and genetic structure in connection with those of its host butterflies in Sweden. To this aim, we gathered data from 428 P. confusa individuals reared from 6094 butterfly larvae (of A. urticae , A. io , and in two occasions of Araschnia levana ) collected over two years (2017 and 2018) and across 19 sites distributed along a 500 km latitudinal gradient. We found that P. confusa is widely distributed along the latitudinal gradient. Its distribution seems constrained over time by the phenology of its hosts. The large variation in climatic conditions between sampling years explains the decrease in phenological overlap between P. confusa and its hosts in 2018 and the 33.5% decrease in the number of butterfly larvae infected. At least in this study, P. confusa seems to favour A. urticae as host. While it parasitized nests of A. urticae and A. io equally, the proportion of larvae parasitized is significantly higher for A. urticae . At the landscape scale, P. confusa is almost exclusively found in vegetated open land and near deciduous forests, whereas artificial habitats are negatively correlated with the likelihood of a nest to be parasitized. The genetic analyses on 89 adult P. confusa and 87 adult A. urticae using CO1 and AFLP markers reveal a low genetic diversity in P. confusa and a lack of genetic structure in both species, at the scale of our sampling. Further genetic studies using high-resolution genomics tools will be required to better understand the population genetic structure of P. confusa , its biotic interactions with its hosts, and ultimately the stability and the functioning of natural ecosystems.
- Published
- 2020
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46. Identification of a combination of transcription factors that synergistically increases endothelial cell barrier resistance.
- Author
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Roudnicky F, Kim BK, Lan Y, Schmucki R, Küppers V, Christensen K, Graf M, Patsch C, Burcin M, Meyer CA, Westenskow PD, and Cowan CA
- Subjects
- Blood-Brain Barrier cytology, Cell Differentiation, Endothelial Cells cytology, Humans, Pluripotent Stem Cells cytology, Endothelial Cells metabolism, Transcription Factors metabolism
- Abstract
Endothelial cells (ECs) display remarkable plasticity during development before becoming quiescent and functionally mature. EC maturation is directed by several known transcription factors (TFs), but the specific set of TFs responsible for promoting high-resistance barriers, such as the blood-brain barrier (BBB), have not yet been fully defined. Using expression mRNA data from published studies on ex vivo ECs from the central nervous system (CNS), we predicted TFs that induce high-resistance barrier properties of ECs as in the BBB. We used our previously established method to generate ECs from human pluripotent stem cells (hPSCs), and then we overexpressed the candidate TFs in hPSC-ECs and measured barrier resistance and integrity using electric cell-substrate impedance sensing, trans-endothelial electrical resistance and FITC-dextran permeability assays. SOX18 and TAL1 were the strongest EC barrier-inducing TFs, upregulating Wnt-related signaling and EC junctional gene expression, respectively, and downregulating EC proliferation-related genes. These TFs were combined with SOX7 and ETS1 that together effectively induced EC barrier resistance, decreased paracellular transport and increased protein expression of tight junctions and induce mRNA expression of several genes involved in the formation of EC barrier and transport. Our data shows identification of a transcriptional network that controls barrier resistance in ECs. Collectively this data may lead to novel approaches for generation of in vitro models of the BBB.
- Published
- 2020
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47. Data Integration for Large-Scale Models of Species Distributions.
- Author
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Isaac NJB, Jarzyna MA, Keil P, Dambly LI, Boersch-Supan PH, Browning E, Freeman SN, Golding N, Guillera-Arroita G, Henrys PA, Jarvis S, Lahoz-Monfort J, Pagel J, Pescott OL, Schmucki R, Simmonds EG, and O'Hara RB
- Subjects
- Models, Theoretical, Biodiversity, Ecology
- Abstract
With the expansion in the quantity and types of biodiversity data being collected, there is a need to find ways to combine these different sources to provide cohesive summaries of species' potential and realized distributions in space and time. Recently, model-based data integration has emerged as a means to achieve this by combining datasets in ways that retain the strengths of each. We describe a flexible approach to data integration using point process models, which provide a convenient way to translate across ecological currencies. We highlight recent examples of large-scale ecological models based on data integration and outline the conceptual and technical challenges and opportunities that arise., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2020
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48. The Genome Sequence of the Eastern Woodchuck ( Marmota monax ) - A Preclinical Animal Model for Chronic Hepatitis B.
- Author
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Alioto TS, Cruz F, Gómez-Garrido J, Triyatni M, Gut M, Frias L, Esteve-Codina A, Menne S, Kiialainen A, Kumpesa N, Birzele F, Schmucki R, Gut IG, and Spleiss O
- Subjects
- Animals, Base Sequence, Cluster Analysis, Disease Models, Animal, Female, Gene Expression Regulation, Marmota immunology, Molecular Sequence Annotation, Open Reading Frames genetics, Phylogeny, Genome, Hepatitis B, Chronic virology, Marmota genetics, Marmota virology
- Abstract
The Eastern woodchuck ( Marmota monax ) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic information on immune pathway genes in this animal model. The woodchuck genome was assembled with a combination of high-coverage whole-genome shotgun sequencing of Illumina paired-end, mate-pair libraries and fosmid pool sequencing. The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of 892 kb, and genome completeness of 99.2%. RNA sequencing (RNA-seq) from seven different tissues aided in the annotation of 30,873 protein-coding genes, which in turn encode 41,826 unique protein products. More than 90% of the genes have been functionally annotated, with 82% of them containing open reading frames. This genome sequence and its annotation will enable further research in chronic hepatitis B and hepatocellular carcinoma and contribute to the understanding of immunological responses in the woodchuck., (Copyright © 2019 Alioto et al.)
- Published
- 2019
- Full Text
- View/download PDF
49. Machine learning-powered antibiotics phenotypic drug discovery.
- Author
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Zoffmann S, Vercruysse M, Benmansour F, Maunz A, Wolf L, Blum Marti R, Heckel T, Ding H, Truong HH, Prummer M, Schmucki R, Mason CS, Bradley K, Jacob AI, Lerner C, Araujo Del Rosario A, Burcin M, Amrein KE, and Prunotto M
- Subjects
- Anti-Bacterial Agents chemistry, Bacteria pathogenicity, Drug Evaluation, Preclinical methods, Humans, Machine Learning, Anti-Bacterial Agents therapeutic use, Bacteria drug effects, Drug Discovery, High-Throughput Screening Assays
- Abstract
Identification of novel antibiotics remains a major challenge for drug discovery. The present study explores use of phenotypic readouts beyond classical antibacterial growth inhibition adopting a combined multiparametric high content screening and genomic approach. Deployment of the semi-automated bacterial phenotypic fingerprint (BPF) profiling platform in conjunction with a machine learning-powered dataset analysis, effectively allowed us to narrow down, compare and predict compound mode of action (MoA). The method identifies weak antibacterial hits allowing full exploitation of low potency hits frequently discovered by routine antibacterial screening. We demonstrate that BPF classification tool can be successfully used to guide chemical structure activity relationship optimization, enabling antibiotic development and that this approach can be fruitfully applied across species. The BPF classification tool could be potentially applied in primary screening, effectively enabling identification of novel antibacterial compound hits and differentiating their MoA, hence widening the known antibacterial chemical space of existing pharmaceutical compound libraries. More generally, beyond the specific objective of the present work, the proposed approach could be profitably applied to a broader range of diseases amenable to phenotypic drug discovery.
- Published
- 2019
- Full Text
- View/download PDF
50. The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcγR) in the Göttingen minipig.
- Author
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Egli J, Schmucki R, Loos B, Reichl S, Grabole N, Roller A, Ebeling M, Odermatt A, and Iglesias A
- Subjects
- Amino Acid Sequence, Animals, Cattle, Humans, Mice, Receptors, IgG analysis, Receptors, IgG chemistry, Swine, Receptors, IgG genetics, Swine, Miniature immunology
- Abstract
Safety and efficacy of therapeutic antibodies are often dependent on their interaction with Fc receptors for IgG (FcγRs). The Göttingen minipig represents a valuable species for biomedical research but its use in preclinical studies with therapeutic antibodies is hampered by the lack of knowledge about the porcine FcγRs. Genome analysis and sequencing now enabled the localization of the previously described FcγRIIIa in the orthologous location to human FCGR3A. In addition, we identified nearby the gene coding for the hitherto undescribed putative porcine FcγRIIa. The 1'241 bp long FCGR2A cDNA translates to a 274aa transmembrane protein containing an extracellular region with high similarity to human and cattle FcγRIIa. Like in cattle, the intracellular part does not contain an immunoreceptor tyrosine-based activation motif (ITAM) as in human FcγRIIa. Flow cytometry of the whole blood and single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) of Göttingen minipigs revealed the expression profile of all porcine FcγRs which is compared to human and mouse. The new FcγRIIa is mainly expressed on platelets making the minipig a good model to study IgG-mediated platelet activation and aggregation. In contrast to humans, minipig blood monocytes were found to express inhibitory FcγRIIb that could lead to the underestimation of FcγR-mediated effects of monocytes observed in minipig studies with therapeutic antibodies.
- Published
- 2019
- Full Text
- View/download PDF
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