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3. Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Author

Pearman, Peter B., Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo C., Aravanopoulos, F. A., Bertola, Laura D., Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela P., Fussi, Barbara, Godoy, José A., Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig R., Raeymaekers, Joost A. M., Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo N., Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank E., Guisan, Antoine, and Bruford, Michael

Published
2024
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8. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource.

Author

Mosca, Elena, Cruz, Fernando, Gómez-Garrido, Jèssica, Bianco, Luca, Rellstab, Christian, Brodbeck, Sabine, Csilléry, Katalin, Fady, Bruno, Fladung, Matthias, Fussi, Barbara, Gömöry, Dušan, González-Martínez, Santiago C, Grivet, Delphine, Gut, Marta, Hansen, Ole Kim, Heer, Katrin, Kaya, Zeki, Krutovsky, Konstantin V, Kersten, Birgit, Liepelt, Sascha, Opgenoorth, Lars, Sperisen, Christoph, Ullrich, Kristian K, Vendramin, Giovanni G, Westergren, Marjana, Ziegenhagen, Birgit, Alioto, Tyler, Gugerli, Felix, Heinze, Berthold, Höhn, Maria, Troggio, Michela, and Neale, David B

Subjects
Abies, Computational Biology, Genomics, Genome, Plant, Databases, Genetic, Genome, Chloroplast, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Genome Size, Whole Genome Sequencing, Abies alba, annotation, chloroplast genome, conifer genome, genome assembly, Genome, Plant, Databases, Genetic, Chloroplast, Genetics
Abstract

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.

Published
2019

9. Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Author

Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank, Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, and Zachos, Frank

Abstract

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union’s Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.

Published
2024

10. Submitted candidate projects for validation as population genetic diversity monitoring.

Author

Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank, Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, and Zachos, Frank

Abstract

A data set of submitted candidate projects for evaluation of validity as Category II population genetic monitoring, with repeated sampling over time and at least one indicator of population genetic diversity., A data set of submitted candidate projects for evaluation of validity as Category II population genetic monitoring, with repeated sampling over time and at least one indicator of population genetic diversity.

Published
2024

25. Genetic variability of pedunculate oak (Quercus robur L.) at the Mediterranean margin of the distribution range

Author

Memišević Hodžić, Mirzeta, Fussi, Barbara, Gömöry, Dušan, and Ballian, Dalibor

Subjects
pedunculate oak, allozyme, genetic variability, marginal populations, rear edge, dob, aloencimi, genetska variabilnost, mejne populacije, zadnji rob, rear edge, allozyme, dob, aloencimi, genetska variabilnost, udc:630*17:630*16, genetic variability, marginal populations, mejne populacije, zadnji rob, udc:630*1, pedunculate oak
Abstract

In Bosnia and Herzegovina, pedunculate oak (Quercus robur L.) occurs at the southern margin of its distribution range, close to the glacial refugia of this species. To assess the patterns of genetic diversity distribution at the rear edge of the Holocene colonization, we studied genetic variation in 20 pedunculate oak populations using 14 allozyme loci. Despite considerable differences among populations, neither the numbers of alleles nor genetic diversity showed any geographical trend within the studied area, although small isolated populations showed generally lower allelic richness. The Bayesian analysis of population structure indicated a kind of geographical pattern. We identified no signs of a recent bottleneck. The proximity to multiple glacial refugia explains the outcomes. Nasl. z nasl. zaslona. Opis vira z dne 23. 12. 2021. Bibliografija: str. 38-40. Abstract.

Published
2022

39. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.):A Community-Generated Genomic Resource

Author

Mosca, Elena, Cruz, Fernando, Gomez-Garrido, Jessica, Bianco, Luca, Rellstab, Christian, Brodbeck, Sabine, Csillery, Katalin, Fady, Bruno, Fladung, Matthias, Fussi, Barbara, Gomory, Dusan, Gonzalez-Martinez, Santiago C., Grivet, Delphine, Gut, Marta, Hansen, Ole Kim, Heer, Katrin, Kaya, Zeki, Krutovsky, Konstantin V., Kersten, Birgit, Liepelt, Sascha, Opgenoorth, Lars, Sperisen, Christoph, Ullrich, Kristian K., Vendramin, Giovanni G., Westergren, Marjana, Ziegenhagen, Birgit, Alioto, Tyler, Gugerli, Felix, Heinze, Berthold, Hoehn, Maria, Troggio, Michela, Neale, David B., Mosca, Elena, Cruz, Fernando, Gomez-Garrido, Jessica, Bianco, Luca, Rellstab, Christian, Brodbeck, Sabine, Csillery, Katalin, Fady, Bruno, Fladung, Matthias, Fussi, Barbara, Gomory, Dusan, Gonzalez-Martinez, Santiago C., Grivet, Delphine, Gut, Marta, Hansen, Ole Kim, Heer, Katrin, Kaya, Zeki, Krutovsky, Konstantin V., Kersten, Birgit, Liepelt, Sascha, Opgenoorth, Lars, Sperisen, Christoph, Ullrich, Kristian K., Vendramin, Giovanni G., Westergren, Marjana, Ziegenhagen, Birgit, Alioto, Tyler, Gugerli, Felix, Heinze, Berthold, Hoehn, Maria, Troggio, Michela, and Neale, David B.

Published
2019

40. GENETIC DIVERSITY AND PARENTAGE ANALYSIS FOR DNA MARKER-BASED FOREST REPRODUCTIVE MATERIAL TRACEABILITY SYSTEM IN LITHUANIA.

Author

KAVALIAUSKAS, Darius, FUSSI, Barbara, SIRGĖDIENĖ, Monika, KEMBRYTĖ, Rūta, and DANUSEVIČIUS, Darius

Subjects
*FOREST restoration, *DNA analysis, *GENETIC variation, *MICROSATELLITE repeats, *SCOTS pine, *SEEDLING quality
Abstract

Scots pine is economically and ecologically important forest tree species in Lithuania. According to the Regulation of Forest Planting and Restoration of Lithuania (2018) and the Regulations on Forest Reproductive Material (FRM) (2017) forests must be planted and replanted with the target tree species, using high quality seeds and seedlings from a given provenance. EU Council Directive (1999/105/EC) indicates that EU Member States are responsible for the regulation, requirements and implementation of FRM quality and traceability system. The existing FRM control system in Lithuania is based on the control actions of the supporting documents regarding the origin of FRM. However, this FRM traceability system is limited and, in some cases, cannot ensure that FRM used for reforestation/afforestation originates from the declared place of origin or belongs to a certain seed or plant lot. In this study we aimed to assess and compare genetic diversity of scots pine seed orchard clones with seeds, and to test DNA based parentage analysis methods with Jonava scots pine seed orchard clones and seeds. Up to now DNA markers based FRM traceability system in Lithuania has not been tested and implemented. Thus, our first results based on 12 nuclear microsatellite markers indicated that genetic diversity among Jonava seed orchard clones and collected seeds were moderately high and comparable with other studies on scots pine in Europe. The test of the maternity analysis software CERVUS has showed very positive results in maternity assignments. Therefore, selected microsatellite markers in combination with accurate sampling design and specific DNA analysis methods should be improved and can be used for FRM traceability system based on DNA “fingerprints”. [ABSTRACT FROM AUTHOR]

Published
2021
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44. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource

Author

Mosca, Elena, primary, Cruz, Fernando, additional, Gómez-Garrido, Jèssica, additional, Bianco, Luca, additional, Rellstab, Christian, additional, Brodbeck, Sabine, additional, Csilléry, Katalin, additional, Fady, Bruno, additional, Fladung, Matthias, additional, Fussi, Barbara, additional, Gömöry, Dušan, additional, González-Martínez, Santiago C, additional, Grivet, Delphine, additional, Gut, Marta, additional, Hansen, Ole Kim, additional, Heer, Katrin, additional, Kaya, Zeki, additional, Krutovsky, Konstantin V, additional, Kersten, Birgit, additional, Liepelt, Sascha, additional, Opgenoorth, Lars, additional, Sperisen, Christoph, additional, Ullrich, Kristian K, additional, Vendramin, Giovanni G, additional, Westergren, Marjana, additional, Ziegenhagen, Birgit, additional, Alioto, Tyler, additional, Gugerli, Felix, additional, Heinze, Berthold, additional, Höhn, Maria, additional, Troggio, Michela, additional, and Neale, David B, additional

Published
2019
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45. Assessment of Genetic Diversity and Population Genetic Structure of Norway Spruce (Picea abies (L.) Karsten) at Its Southern Lineage in Europe. Implications for Conservation of Forest Genetic Resources

Author

Stojnić, Srđan, primary, V. Avramidou, Evangelia, additional, Fussi, Barbara, additional, Westergren, Marjana, additional, Orlović, Saša, additional, Matović, Bratislav, additional, Trudić, Branislav, additional, Kraigher, Hojka, additional, A. Aravanopoulos, Filippos, additional, and Konnert, Monika, additional

Published
2019
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48. On the use of the L1 in beginner’s English and French language classrooms

Author

Fussi, Barbara

Abstract

Die Verwendung der Muttersprache im Fremdsprachenunterricht ist ein viel diskutiertes Thema in der Sprachdidaktik. Im Laufe des 20. Jahrhunderts wurde die Rolle der Muttersprache größtenteils ignoriert, was implizierte, dass die exklusive Verwendung der Zielsprache die beste Methode ist, um Fremdsprachen zu unterrichten. Allerdings wird dieses Prinzip von Einsprachigkeit zunehmend kritisiert und immer mehr ForscherInnen betonen, dass die Muttersprache ein wertvolles Werkzeug für das Lehren und Lernen von Fremdsprachen sein kann. Diese Fallstudie erforscht Englisch- und Französisch-Anfängerunterricht in Österreich und untersucht die Verwendung der Muttersprache im Unterricht und die Ansichten gegenüber dieser bei FremdsprachenlehrerInnen. Daten wurden in LehrerInneninterviews und Unterrichtshospitationen gesammelt und mit Hilfe der qualitativen Inhaltsanalyse ausgewertet. Die Resultate zeigen, dass die FremdsprachenlehrerInnen in dieser Studie an die Notwendigkeit einer größtmöglichen Verwendung der Zielsprache glauben, damit Spracherwerb stattfinden kann. LehrerInnen verwenden die Muttersprache vor allem, um Grammatik zu unterrichten, um eine persönliche Beziehung zu den SchülerInnen aufzubauen, um SchülerInnen zu disziplinieren und um über Themen zu sprechen, die nicht direkt den Fremdsprachenunterricht betreffen. Das Ziel, welches LehrerInnen mit ihrer Sprachwahl verfolgen, ist zuallererst das Verständnis bei den SchülerInnen zu sichern. Weitere Gründe für die Verwendung der Muttersprache sind Zeitersparnis und die Schaffung einer guten Lernumgebung. Zusätzlich werden in dieser Arbeit interne und externe Faktoren aufgezeigt, die die LehrerInnen in ihren Entscheidungen beeinflussen. Die Natur der Zielsprache kann als Einflussfaktor für den Sprachgebrauch bei LehrerInnen ausgeschlossen werden. Das Können der SchülerInnen und Ansichten gegenüber erfolgreichem Spracherwerb haben einen deutlichen größeren Einfluss auf die Verwendung der Muttersprache bei LehrerInnen., The use of the first language in the foreign language classroom is a controversial issue in language teaching methodology. Throughout the 20th century, the role of the mother tongue was largely ignored, suggesting that target language exclusivity is the preferable way of teaching a foreign language. This monolingual principle is increasingly challenged, and it is suggested that the first language is a valuable resource beneficial for foreign language teaching and learning. This case study explores beginners’ English and French language classrooms and investigates Austrian teachers’ beliefs and practices of first language use. The analysis of teacher interviews and classroom observations shows that the first language serves pedagogical and communicative functions. The results demonstrate that language teachers of this study believe in the need for maximal use of the target language to allow for successful language acquisition. The first language is predominantly used by teachers for teaching grammar, establishing a personal relationship, disciplining students, and discussing non-school related issues. The goal teachers pursue with their language choice is primarily to ensure comprehension, in addition to saving time, and creating a supportive learning environment. Various internal and external factors have been identified to influence teachers. The nature of the target language can be eliminated as a variable. Students’ proficiency and teachers’ beliefs about second language acquisition have a much greater impact on teachers’ use of the first language.

Published
2017
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49. The Interplay between Forest Management Practices, Genetic Monitoring, and Other Long-Term Monitoring Systems

Author

Kavaliauskas, Darius, primary, Fussi, Barbara, additional, Westergren, Marjana, additional, Aravanopoulos, Filippos, additional, Finzgar, Domen, additional, Baier, Roland, additional, Alizoti, Paraskevi, additional, Bozic, Gregor, additional, Avramidou, Evangelia, additional, Konnert, Monika, additional, and Kraigher, Hojka, additional

Published
2018
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