Učni načrt predmeta

Predmet:

Metodologije v raziskavah biotske pestrosti

Course:

Biodiversity research metodology

Študijski program in stopnja / Study programme and level	Študijska smer / Study field	Letnik / Academic year	Semester / Semester
Nanoznanosti in nanotehnologije, 3. stopnja	Bioznanosti	1	1
Nanosciences and nanotechnologies, 3rd cycle	Biosciences	1	1

Vrsta predmeta / Course type

Izbirni / Elective

Univerzitetna koda predmeta / University course code:

NANO3-936

Predavanja Lectures	Seminar Seminar	Vaje Tutorial	Klinične vaje work	Druge oblike študija	Samost. delo Individ. work	ECTS
30	30			30	210	10

*Navedena porazdelitev ur velja, če je vpisanih vsaj 15 študentov. Drugače se obseg izvedbe kontaktnih ur sorazmerno zmanjša in prenese v samostojno delo. / This distribution of hours is valid if at least 15 students are enrolled. Otherwise the contact hours are linearly reduced and transfered to individual work.

Nosilec predmeta / Course leader:

doc. dr. Al Vrezec

Sodelavci / Lecturers:

prof. dr. Matjaž Kuntner , dr. Nataša Mori , dr. Jernej Polajnar , dr. David Stanković , dr. Rok Šturm , doc. dr. Anamarija Žagar , doc. dr. Alenka Žunič-Kosi

Jeziki / Languages:

Predavanja / Lectures:

slovenščina, angleščina / Slovenian, English

Vaje / Tutorial:

Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:

Prerequisites:

Zaključen študij druge stopnje ustrezne (naravoslovne ali tehniške) smeri ali zaključen študij drugih smeri z dokazanim poznavanjem osnov področja predmeta (pisna dokazila, pogovor).

Completed second level studies in natural sciences or engineering or completed second level studies in other fields with proven knowledge of fundamentals in the field of this course (certificates, interview).

Vsebina:

Content (Syllabus outline):

Preučevanje biotske pestrosti je v veliki meri povezano s preučevanjem njenega pospešenega upada in razumevanje ekosistemskih storitev, zaradi česar je metodologija za raziskovanje le-te v preteklih letih doživela skokovit razvoj, ki omogoča zbiranje in analizo velikih nizov podatkov, napredno statistično sklepanje in razvoj natančnih napovednih modelov. Slednji so ključni za razumevanje delovanja ekosistemov, ekoloških procesov in biotskih okoljskih sprememb. Predmet bo podiplomskim študentom zagotovil pregled konvencionalnih kot tudi najnaprednejših pristopov za preučevanje biotske pestrosti:
- zasnova terenskih raziskav,
- biološke zbirke in podatki o biotski pestrosti,
- konvencionalne metode za monitoring biodiverzitete,
- monitoring biodiverzitete celinskih vod – površinske in podzemne vode,
- ekofiziologija,
- metodologije v kemični ekologiji,
- ekotremologija in ekoakustika,
- filogenetska sistematika,
- varstvena genomika,
- tehnologija okoljske DNK,
- mehanistični pristopi v ekološkem modeliranju,
- koncipiranje dolgoročnih raziskav v ekologiji,
- občanska znanost v biodiverzitetnih raziskavah.

Accelerated biodiversity decline and understanding of ecosystem services has driven the development of advanced tools and methodologies, enabling more comprehensive and efficient study of this topic. These advancements facilitate the collection and analysis of large datasets, support advanced statistical inference, and enable the creation of precise predictive models. This is key for understanding ecosystem function, ecological processes and biotic environmental changes. The subject offers postgraduate students a thorough overview of both traditional and innovative approaches to biodiversity research, including:
- Design of field studies,
- Biological collections and biodiversity data,
- Conventional methods for biodiversity monitoring,
- Biodiversity monitoring of inland waters – surface and groundwater,
- Ecophysiology,
- Methods in chemical ecology,
- Ecotremology and ecoacoustics,
- Phylogenetic systematics,
- Conservation genomics,
- Environmental DNA technology,
- Mechanistic approaches in ecological modeling,
- Conceptualization of long-term ecological studies,
- Citizen science in biodiversity research.

Temeljna literatura in viri / Readings:

Knjige / books:
- Allendorf, F.W., Funk, W. C., Aitken, S. N., Byrne, M., & Luikart, G. (2022) Conservation and the Genomics of Populations. 3rd Edition. Oxford University Press, Oxford.
- Brower, James E., Zar, J. H. & Von Ende C. N. (1998) Field and laboratory methods for general ecology. Vol. 4. WCB McGraw-Hill, Boston.
- Chave, P. (2007. The EU Water Framework Directive - An Introduction, IWA; DOI: 10.2166/9781780402239.
- Farina, A. & Gage S. H. (2017) Ecoacoustics. John Whily and Sons, Oxford.
- Hill P. S.M., Lakes-Harlan, R., Mazzoni, V., Narins, P.M., Virant-Doberlet, M., Wessel, A. (2019) Biotremology: Studying Vibrational Behavior. Springer Nature Link.
- Moyes, C.D. & Schulte, P.M., (2005) Animal Physiology. Benjamin Cummings, San Francisco.
- Sutherland W.J. (2000): The conservation handbook: research, management and policy. Blackwell Science, Oxford.
- Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018) Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press, Oxford
- Tscharntke T., Hawkins B.A. (2002) Multitrophic Level Interactions. Cambridge University Press, Cambridge.
- Wyatt, T. D. (2014). Pheromones and animal behavior: Chemical signals and signatures (2nd ed.). Cambridge University Press.
- Haynls K.F. & M illar J.G. (eds): Methods in chemical ecology. VOL. 2. Bioassay methods. Chapman & Hall, Kluwer Academic Publishers

Revije / Journals:

- Gavioli, A., Filipe, A. F., Patonai, K., Milardi, M., & Castaldelli, G. (2023). Effectiveness of the Natura 2000 network for freshwater fish conservation in a Mediterranean region. Frontiers in Environmental Science, 11: 1122464. https://doi.org/10.3389/fenvs.2023.1122464
- Griebler, C., Stein, H., Kellermann, C., Berkhoff, S., Brielmann, H., Schmidt, S., Selesi, D., Steube, C., Fuchs, A. & Hahn, H. J. (2001) Ecological assessment of groundwater ecosystems – Vision or illusion? Ecological Engineering, 36: 1174-1190, https://doi.org/10.1016/j.ecoleng.2010.01.010.
- Jørgensen , L.F. and Stockmarr, J., 2009. Groundwater monitoring in Denmark: Characteristics, perspectives and comparison with other countries, Hydrogeology Journal ) 17: 827–842 https://doi.org/10.1007/s10040-008-0398-7
- Kearney, M.R. and Porter, W.P. (2020) NicheMapR–an R package for biophysical modelling: the ectotherm and dynamic energy budget models. Ecography, 43: 85-96.
- Klink van R. et al. (2022). Emerging technologies revolutionise insect ecology and monitoring. Trends in Ecology and Evolution, 37: 872-885.
- Meineke, E. K., Davies, T. J., Daru, B. H., & Davis, C. C. (2019). Biological collections for understanding biodiversity in the Anthropocene. Philosophical Transactions of the Royal Society B, 374: 20170386. https://doi.org/10.1098/rstb.2017.0386.
Schlick-Steiner, B. C., Steiner, F. M., Seifert, B., Stauffer, C., Christian, E., & Crozier, R. H. (2010). Integrative taxonomy: a multisource approach to exploring biodiversity. Annual review of entomology, 55: 421-438.

Cilji in kompetence:

Objectives and competences:

Splošni cilj predmeta je priprava podiplomskih študentov za raziskovalno delo na področju biodiverzitetnih raziskav. Posamezni cilji predmeta pa so:
- poznavanje relevantnih konceptov, ki so ključni za zanesljivo zbiranje kvantitativnih podatkov na terenu (statistično relevanten vzorec, priprava vzorčnih protokolov, beleženje, organizacija in sledljivost podatkov);
- razumevanje pomena in postopkov upravljanja in uporabe zbirk biološkega materiala (od klasičnih muzejskih zbirk do kriozbirk), poznavanja ključne terminologije v muzeologiji in poznavanje (in uporaba) prosto dostopnih biodiverzitetnih podatkov;
- ponuditi praktičen in osnovni pregled uveljavljenih (konvencionalnih) pristopov monitoringa biodiverzitete glede na ciljna vzorčenja različnih skupin organizmov od vretenčarjev, nevretenčarjev do rastlin;
- seznanitev z obstoječimi shemami monitoringov celinskih voda (ekološko stanja in ekološki potencial) ter predstavitev Natura 2000 naravovarstvene sheme v povezavi s celinskimi vodami;
- predstavitev veljavnega monitoringa podzemnih voda (spremljanje količinskega in kakovostnega stanja) in koncepta v razvoju: monitoring ekološkega stanja podzemnih voda;
- poznavanje ključnih konceptov v (živalski) ekofiziologiji s primeri eksperimentalnih in in situ raziskav na kopenskih ektotermnih organizmih;
- zbiranje, analiza in interpretacija kemičnih signalov v ekosistemih za raziskovanje kemične komunikacije ter ekoloških interakcij med organizmi;
- koncept vibracijske krajine in uporaba vibracij biološkega izvora za preučevanje biodiverzitete s poudarkom na žuželkah;
- koncept zvočne krajine in uporaba živalskega oglašanja za preučevanje biodiverzitete ter ciljni monitoring varstveno pomembnih vrst
- teoretično ozadje in koncepti pridobivanja in interpretiranja filogenij ter njihova uporaba v sistematski biologiji vključno z integrativno taksonomijo;
- pregled uporabe aplikacij genomskih tehnologij za bolj učinkovito varovanje upravljanje z ogroženimi vrst;
- poznavanje koncepta okoljske DNK in uporaba te za detekcijo tarčnih organizmov in karakterizacijo celotnih združb;
- pregled različnih pristopov modeliranja v ekologiji in uporaba prosto dostopnih orodij in baz podatkov za biofizikalno mehanistično modeliranje;
- razumevanje koncepta in pomena dolgoročnih ekoloških raziskav za dolgotrajen vpogled v dinamiko ekosistemov pod vplivom podnebnih, okoljskih in drugih sprememb, vključujoč populacijsko soodvisnost vrst na cehovskem ali multitrofičnem nivoju;
- poznavanje pomena, potenciala in omejitve občanske znanosti v biodiverzitetnih raziskavah.

Študenti bodo pridobili kompetence na področju izvajanja sodobnih biodiverzitetnih raziskav vključno s seznanitvijo z monitoringi biodiverzitete v sklopu zakonodajnih okvirov. Okrepili bodo tehnično znanje in praktične veščine za izvajanje biodiverzitetnih raziskav na svojem osnovnem področju. Poleg tega bodo razvijali komunikacijske spretnosti pri podajanju raziskav v javnosti in razvijali kritično in samokritično presojo.

The objective of this course is to prepare postgraduate students for research work in the field of biodiversity research. This comprehensive course equips students with both theoretical knowledge and practical skills for advanced biodiversity research and monitoring. The specific objectives include:
- Understanding key concepts essential for reliable collection of quantitative field data, including statistically significant sampling, preparation of sampling protocols, data recording, organization, and traceability.
- Comprehending the importance and procedures for managing and utilizing biological material collections, from traditional museum collections to cryo-collections, understanding key terminology in museology, and using open-access biodiversity data.
- Providing a practical overview of established (conventional) biodiversity monitoring approaches for targeted sampling of various organism groups, including vertebrates, invertebrates, and plants.
- Familiarizing students with existing monitoring frameworks for inland waters, including assessments of ecological status and ecological potential, as well as an overview of the Natura 2000 conservation scheme in the context of inland waters.
- Introducing groundwater monitoring schemes (quantitative and qualitative status assessment) and familiarization with the emerging concept of monitoring of the ecological state in groundwaters.
- Understanding key concepts in animal ecophysiology, with examples of experimental and in-situ research on terrestrial ectothermic organisms.
- Collection, analysis, and interpretation of chemical signals in ecosystems for researching chemical communication and ecological interactions between organisms.
- The concept of vibrational landscapes and the use of biologically derived vibrations for biodiversity studies, with an emphasis on research in insects.
- The concept of soundscape and the use of animal vocalizations for biodiversity studies and targeted monitoring of species of conservational importance.
- Theoretical background and concepts of phylogeny reconstruction and interpretation, and their application in systematic biology, including integrative taxonomy.
- Exploring the applications of genomic technologies to enhance conservation and management of endangered species.
- Understanding the concept of environmental DNA (eDNA) and overview of its use in detecting target organisms and characterizing entire communities.
- Reviewing various ecological modelling approaches and using open and free tools and databases for biophysical mechanistic modelling.
- Understanding the concept and importance of long-term ecological research for gaining insights into ecosystem dynamics under the influence of climate, environmental, and other changes, including population interdependencies at guild or multitrophic levels.
- Recognizing the significance, potential and limitations of citizen science in biodiversity research.

Students will acquire competences in conducting advanced biodiversity research, including biodiversity monitoring within legislative frameworks. They will enhance their technical knowledge and practical skills for carrying out biodiversity research in their primary field of expertise. Additionally, students will develop communication skills for presenting research in public forums and foster critical and self-critical thinking.

Predvideni študijski rezultati:

Intendeded learning outcomes:

Študenti bodo dobili celovit pregled nad metodami in tehnologijami za preučevanje biotske pestrosti, osvojili bodo napredno izrazoslovje, se seznanili z najnaprednejšimi pristopi in razširili znanje o vsakem od opredeljenih področji. Poleg tega bo v sklopu seminarjev posebna pozornost posvečena osnovnemu raziskovalnemu področju posameznega študenta, s čimer bodo poglobili svoje ekspertize znotraj izbranih območij vezanem na biodiverziteto. V seminarjih bodo študenti osvojili raziskovalne metode na svojem osnovnem področju in pokazali sposobnost uporabe pridobljenega znanja in spretnosti pri izvedbi analiz in obdelavi podatkov v praksi. Na ta način bomo študente opremili s tehničnim in metodološkim znanjem in jih pripravili za kritično evalvacijo in vpeljevanjem inovativnih pristopov v lastne projekte na področju biodiverzitetnih raziskav in vrednotenj.

Students will gain a comprehensive overview of methods and technologies for studying biodiversity, master advanced terminology, become familiar with state-of-the-art approaches, and expand their knowledge in the defined areas. In addition, seminars will place special focus on individual research fields of each student, allowing them to deepen their expertise in their chosen area connected to biodiversity. Through these seminars, students will acquire research methods relevant to their field of study and demonstrate the ability to apply the knowledge and skills gained to perform practical analyses and data processing. This approach not only equips students with technical and methodological proficiency but also prepares them to critically evaluate and adapt innovative research techniques to their own projects at the field of biodiversity research and assessments.

Metode poučevanja in učenja:

Learning and teaching methods:

Interaktivno delo s študenti v obliki predavanj, terenskih ogledov in praktičnega izvajanja tekom priprave seminarske naloge. Predstavitve seminarjev z moderirano debato in zagovorom – predstavitve bodo potekala javno oz. v prisotnosti izvajalcev predmeta, drugih študentov in ostalih vabljenih z namenom vaje javnega nastopanja in vzpostavljanja medsebojnega sodelovanja pri obravnavi sorodnih tematik. Poudarek je predvsem na reševanju znanstvenih vprašanj iz osnovnega področja posameznega študenta vezanih na biodiverziteto.

Interactive engagement with students will include lectures, field visits, and hands-on work during the preparation of seminar papers. Seminar presentations will be followed by moderated debates and the defence of the seminar work. Seminars will be presented, i.e. in the presence of course instructors, fellow students, and invited guests. This approach aims to provide students with practice in public speaking while fostering collaboration on related topics. The focus will primarily be on addressing scientific questions within each student’s primary field of study associated with biodiversity.

Načini ocenjevanja:

Delež v % / Weight in %

Assesment:

Seminar

60 %

Seminar

Ustni zagovor seminarja

40 %

Oral defense of seminar work

Reference nosilca / Lecturer's references:

1.	1. KADEJ, Marcin, ZAJĄC, Krzysztof, GUTOWSKI, Jerzy M., JAWORSKI, Tomasz, PLEWA, Radosław, RUTA, Rafał, SIKORA, Katarzyna, SMOLIS, Adrian, MAGOGA, Giulia, MONTAGNA, Matteo, KAPLA, Andrej, VREZEC, Al, et al. Disentangling phylogenetic relations and biogeographic history within the Cucujus haematodes species group (Coleoptera: Cucujidae). Molecular phylogenetics and evolution. Aug. 2022, vol. 173, [1]-19 str., ilustr. ISSN 1055-7903. https://doi.org/10.1016/j.ympev.2022.107527, DOI: 10.1016/j.ympev.2022.107527
2.	2. ŽLABRAVEC, Zoran, VREZEC, Al, SLAVEC, Brigita, KUHAR, Urška, ZORMAN-ROJS, Olga, RAČNIK, Joško. Herpesvirus infection in a breeding population of two coexisting strix owls. Animals. 2021, vol. 11, no. 9, art. 2519, str. 1-11. ISSN 2076-2615. https://www.mdpi.com/2076-2615/11/9/2519, Repozitorij Univerze v Ljubljani – RUL, DOI: 10.3390/ani11092519
3.	3. PETRAS, Tina, VREZEC, Al. Modelling population dynamics and trends in migratory birds from non-standardized multi-species ringing data : the potential of multi-model selection. Bird study : the journal of the British trust for ornithology. 2021, vol. 68, no. 3, str. 330–344. ISSN 0006-3657. https://doi.org/10.1080/00063657.2022.2026876, DOI: 10.1080/00063657.2022.2026876
4.	4. THOMAES, Arno, BARBALAT, Sylvie, BARDIANI, Marco, BOWER, Laura, CAMPANARO, Alessandro, SLEZIAK, Natalia Fanega, SOUTINHO, João Gonçalo, GOVAERT, Sanne, HARVEY, Deborah J., HAWES, Colin, KADEJ, Marcin, MÉNDEZ, Marcos, MERIGUET, Bruno, RINK, Markus, ROSSI DE GASPERIS, Sarah, RUYTS, Sanne, ŠERIĆ-JELASKA, Lucija, SMOLIS, Adrian, SNEGIN, Eduard, TAGLIANI, Arianna, VREZEC, Al. The European stag beetle (Lucanus cervus) Monitoring network: international citizen science cooperation reveals regional differences in phenology and temperature response. Insects. 2021, vol. 12, iss. 9, str. 1-14, ilustr. ISSN 2075-4450. https://www.mdpi.com/2075-4450/11/12/896, DiRROS - Digitalni repozitorij raziskovalnih organizacij Slovenije, dCOBISS, DOI: 10.3390/insects12090813
5.	5. TOME, Davorin, DENAC, Damijan, VREZEC, Al. Mowing is the greatest threat to Whinchat Saxicola rubetra nests even when compared to several natural induced threats. Journal for nature conservation. Apr. 2020, vol. 54, [article] 125781, str. 1-8, ilustr. ISSN 1617-1381. DOI: 10.1016/j.jnc.2019.125781