News

Participation on SRCE-DEI2024

The annual conference SRCE Days of e-Infrastructure 2024 was held from 16-19 April in the Rectorate of the University of Zagreb and at the University Computing Center. Meeting brought together professors, assistants, professional staff and employees in the science and higher education.
Our collaborator on the project, Maja Mucko, Ph.D., was a lecturer in the thematic block "Supercomputers in research and teaching: How can SRCE help you?", and she presented examples from the practice of the workshops she previously held at the University of Zagreb and the University of Sarajevo in cooperation with SRCE, using the high performance computing services. The lecture "Unix in education for biologists: practical examples" is available on the conference website. Previously held workshops presented in the lecture disseminated the Croatian Science Foundation projects "AmphiAdriPlant" (UIP-2017-05-2882), "Island" (IP-2020-02-9524) and the COST action "Ocean4Biotech" (CA18238).


During third day of the Conference, Maja Mucko, Ph.D., also held a 180-minute workshop "NGS data processing with the QIIME2 software package: examples from practice". A total of 10 participants of the workshop from various institutions (University of Zagreb, Institute of Sea and Coasts of the University of Dubrovnik and Institute of Oceanography and Fisheries, Split) learned to use the QIIME2 software package in the processing of NGS data provided by the TurtleBIOME project (Caretta caretta endozoic and spizoic microbiome). The workshop was interactive, dynamic and fully based on SRCE high performance computing resources, with technical support from e-scientists, mag. Marko Hrženjak.



The final, 15th project meeting was held on December 11, 2023 in the premises of the Faculty of Forestry and Wood Technology, Svetošimunska cesta 23. The meeting was attended live by members of the research team: Ph.D. Ivana Rešetnik, associate professor, Ph.D. Ivica Ljubičić, Ph.D. Ana Terlević and collaborators on the project, associate professor, Ph.D. Sandro Bogdanović, assistant professor, Ph.D. Martina Temunović and Ph.D. Maja Mucko. At the meeting, ongoing dissemination, the results of data analysis so far, and a plan for the remaining period of the project were discussed.


Dissemination of project results at a two-day COST action CA18238 "Ocean4biotech" workshop at the University of Sarajevo


From 17.01.2024. to 18.01.2024., a workshop of COST action CA 18238 was held in the premises of the Holiday Hotel and the University of Sarajevo, Faculty of Science. During the first day of the workshop, Maja Mucko, Ph.D., held an invited lecture entitled "Introduction to bioinformatics: from experimental design to pretty plots", while on the second day of the workshop she led a practical workshop for students and members of the COST action in the premises of the computer lab of the Mathematics Department of the Faculty of Science in Sarajevo. For the purposes of the practical workshop, data from projects ISLAND IP-2020-02-9524 and AmphiAdriPlant UIP-2017-05-2882, on which Maja Mucko works as collaborator, were used. The workshop was also supported by the University Computing Center "SRCE", which provided a virtual cluster and modules for bioinformatics analysis.

The participants learned how to align DNA sequences in the ClustalW2 UNIX-based program, to create a Maximum Likelihood phylogeny using the IQ-TREE program and to visualize and interpret data using the FigTree program and the R programming language. Also, participants learned the basics of the UNIX system while working inside a computer server.


On September 29 and October 3, 2023, postdoctoral fellow Ana Terlević, PhD Maja Mucko and PhD Ivana Rešetnik participated in the workshop "Access and use of advanced computing resources Supek and Vrančić”. The workshop was organized by the University of Zagreb, University Computing Center Srce.

Project workshop UNIX for bioinformatics in processing of genetic data

From 1st to 3rd of March, 2023. in the premises of the Faculty of Forestry and Wood Technology, a project workshop on the use of the UNIX system in the bioinformatics processing of genetic data generated within the AmphiAdriPlant project was held. 
The project workshop was supported by the University Computing Center "SRCE", which provided a virtual cluster and modules for the bioinformatical analyses. The participants were collaborators of the AmphiAdriPlant project, as well as interested employees and students of the Biology Department of the Faculty of Science, University of Zagreb and one participant from the Institute of Oceanography and Fisheries, Split.
The main lecturer was Maja Mucko, Ph.D., a post-doctoral fellow at the Botanical dividion of the Biological Department of the Faculty of Science, while Marko Kvakić, Ph.D. and mag.agr. Marko Hrženjak participated in the last day of the workshop where they presented the existing advanced computing services, the upcoming Galaxy service for bioinformatics analysis, and the new computing resources of the HR-ZOO project that will be presented at the DEI 2023 conference in March (March 28-30, 2023; information at: https://dei.srce.hr/#_blank).
The participants learned how to de-novo assemble RADseq data through the STACKS program, create a Maximum Likelihood phylogeny using the IQ-TREE program, and analyze the structure of genetic data using the Structure and fastStructure softwares. Also, the participants learned to write scripts for the previously mentioned programs and the MrBayes program for Bayesian phylogeny, for setting jobs on the Isabella computing cluster, available to users within the academic community.

14th project meeting

The 14th project meeting was held on January 16, 2023 in the premises of the Faculty of Forestry and Wood Technology, Svetošimunska cesta 23. The meeting was attended live by members of the research team: Ph.D. Ivana Rešetnik, associate professor, Ph.D. Ivica Ljubičić, Ph.D. Ana Terlević and collaborators on the project, associate professor, Ph.D. Sandro Bogdanović, assistant professor, Ph.D. Martina Temunović and Ph.D. Maja Mucko. Ongoing dissemination and papers were discussed and team delivered a plan for the remaining period of the project.

Ph.D. Ana Terlević successfully defended her doctoral dissertation

The doctoral student Ana Terlević successfully defended her doctoral dissertation entitled "Phylogeography and taxonomy of Dianthus sylvestris Wulfen s.l. on the Balkan Peninsula" on December 21, 2022, in the premises of the Biological Department of the Faculty of Sciencein Zagreb. The committee for the defense of the doctoral dissertation, consisting of:
Prof. Ph.D. Zlatko Liber, PMF, Zagreb
Prof. Ph.D. Peter Schönswetter, University of Innsbruck, Innsbruck, Austria
Asst. Ph.D. Martina Temunović, Faculty of Forestry and Wood Technology, Zagreb
rated Ana's dissertation as excellent and the defense as successful, which earned Ana Terlević the academic degree of Doctor of Science in the scientific field of natural science, the scientific field of biology, as well as all the rights to which she is entitled according to the regulations.

Congratulations! 

 

 

13th project meeting

The 13th project meeting was held on October 27, 2022, at the Faculty of Forestry and Wood Technology, Svetošimunska cesta 23. The meeting was attended live by members of the research team: project leader, Dr Ivana Rešetnik; associate professor, Dr Ivica Ljubičić; PhD student Ana Terlević and collaborators: Associate Prof. Dr Sandro Bogdanović, assistant professor, Dr Martina Temunović and Dr Maja Mucko. The current state of work tasks, the plan for the future project period and the ongoing analyzes and disseminations were presented at the meeting.

Genome size measurement of new samples of the genus Festuca and demographic analysis of the genus Dianthus


From October 13 to 26, the project leader, Dr Ivana Rešetnik and collaborator on the project Dr Martina Temunović stayed at the Institute of Botany of the University of Innsbruck (Austria). During their stay, they measured the genome sizes of newly collected samples of the genus Festuca and analyzed the demography of the genus Dianthus with the DADI tool. 

Postdoctoral student Maja Mucko at the ForBIO workshop, Drꬾbak, Norway

From 7th to 14th October , 2022, postdoctoral fellow Maja Mucko participated in a workshop organized by ForBIO on the topic "Population genetics of polyploids, from theory to practice". The workshop was attended by 14 participants and 6 teachers, renowned scientists from the field of population genetics of polyploid organisms from all over the world. The workshop itself was held under the full sponsorship of the University of Oslo and the organization ForBIO.
The workshop covered various topics, from the theory of population genetics and statistical population parameters, analysis of population data with the programs PolyGene, Structure and the programming language R (adegenet package), to the detection of candidate genes that participate in adaptive strategies of populations. This workshop also had an introductory one-day symposium that took place online in March this year, and will have a follow-up symposium in online form in March 2023. for reasons of keeping the scientific community active.
The postdoctoral student successfully mastered the exercises at the workshop and presented the assigned project with a powerpoint presentation.


Festuca field research

In the period from June 28th to July 4th, 2022, members of the project team collected four populations of the genus Festuca. Festuca xanthina was collected from the locus classicus near Băila Herculana in Romania, while F. cyllenica was collected from the locus classicus on Mount Kyllini in the Peloponnese. The last-mentioned species was also collected on Mount Olympus and Dirfi in Greece.

The 12th project meeting was held on April 1, 2022 in the premises of the Department of Biology, Marulićev trg 20. The meeting was attended live by members of the research team: Dr Ivana Rešetnik, Associate Professor, Dr Ivica Ljubičić, postdoctoral fellow Dr Maja Mucko, PhD student Ana Terlević and project associate Associate Professor Dr. Sandro Bogdanović. The current state of work tasks, the plan for the future project period and the ongoing analyzes and disseminations were presented at the meeting.

PhD student Ana Terlević attended the Transmitting Science course “Introduction to Bayesian Inference in Practice”. The course was delivered live online on Zoom platform from April 4th to 8th, 2022, and it provided relevant concepts and basic theory of Bayesian inference, with the focus being to learn how to do it in practice by writing the code. PhD student learned how to implement the most common algorithm to estimate parameters based on posterior probabilities, that is Markov Chain Monte Carlo samplers, using R software. The course was led by computational biologist Dr. Daniele Silvestro from the University of Fribourg (Switzerland) and Tobias Andermann from the University of Gothenburg (Sweden).

Dr Ivana Rešetnik, Dr Martina Temunović and Dr Maja Mucko participated in an online workshop entitled "RADseq for phylogenOMICs" organized by the Albrecht-Haller-Institute for Plant Sciences, University of Goettingen. The workshop was held during April 5 th and 6 th, 2022 from 10 am to 5 pm, and the program included numerous topics from population genetics and RADseq sequencing, as well as data processing with available programs and tools. Participants received an overview of the RADseq methodology and library preparation for NGS sequencing; data processing via STACKS and ipyrad programs; analysis of hybrid zones; usage of data obtained by RADseq method for phylogenetic tools and their analyses; of combining RADseq and WGS (whole genome sequencing) data; building of phylogenetic networks with SNP data and Bayesian genotyping in polyploid species by the polyRAD method.

Postdoctoral fellow dr.sc. Maja Mucko participated in the course "Statistical Analyzes with R" organized by the Transmitting Science Group from 21 to 25 February 2022. The course was held entirely online, a total of 26 hours. The course included presentations and exercises in the programming language R while the topics were univariate and multivariate statistical analysis. Lectures and exercises were organized through four modules, and participants learned:

  • load and prepare data for analysis using the tidyverse, dplyr, readxl and readr packages;
  • explore data through variation, co-variation, normal data distribution, outlier detection,
  • test data with linear regressions, co-linearity, homogeneity of variance, interactions and independence of variables
  • test data by statistical methods such as linear regression, ANOVA, using generalized linear models and additive models
  • create (draw) graphs using the ggplot2 package
  • calculate and draw 'unconstrained' PCA and nMDS and 'constrained' RDA and CCA multivariate statistical analyzes using the vegan and ade4 packages.

The postdoctoral student won the award for the best student in the course, for which she will also receive a special award.

Postdoctoral fellow, Dr Maja Mucko participated in the course "RADseq data analysis" organized by Physalia (Berlin, Germany) from 8 to 12 November 2021.
The course included exercises in Linux within the Amazon server; lectures and practical work of of de_novo assembly of genetic data in order to identify polymorphic variants within the genome (SNPs); identification SNPs according to reference genomes mapping; and work with genotypic data after processing sequences obtained by next generation sequencing on the Illumina platform. The course lasted a total of 30 hours. The knowledge gained in this course will enable obtaining key segments of the project because it is based on the processing of genetic data and analyses on the genera Festuca and Dianthus.


Doctoral students Marko Doboš and Ana Terlević stayed stayed at the University of Innsbruck, Institute of Botany (Austria) from September 19th to October 2nd, 2021, where they worked with a flow cytometer.
Work was done in collaboration with the research group Evolutionary Systematics led by Prof. Peter Schönswetter.

The relative genome size Dianthus sylvestris and Festuca bosniaca species collected during field work in 2021 was measured by flow cytometry.

The aim of these measurements is to assess the degree of ploidy of the samples and to determine the variability of genome size between the populations collected in the Balkans. A total of ~190 samples from the Festuca bosniaca species complex and ~300 samples from the Dianthus sylvestris species complex were measured. 

The stay of doctoral students in Innsbruck was also achieved thanks to a bilateral Croatian-Austrian project that investigates the evolution of genome size and polyploidization into D. sylvestris species, and whose leader is Prof. Dr. Sandro Bogdanović.

11th project meeting 


The 11th project meeting was held on September 13th, 2021 in the premises of the Faculty of Agriculture (Svetošimunska cesta 25).
The meeting was attended live by members of the research team: Dr Ivana Rešetnik, Dr Ivica Ljubičić, postdoctoral fellow, Dr Maja Mucko, PhD students Ana Terlević and Marko Doboš and associates on the project Dr Sandro Bogdanović and Dr Martina Temunović (who joined via the zoom platform).
At the meeting were presented following points: current status of work tasks, a report for the previous project period (last project year) and work plans for future processing of data collected in field research during July and August and also plans for future dana analyses and dissemination.

PhD student Ana Terlević participated in an online course organized by Transmitting Science, entitled “Environmental variables: how to obtain and process them with R”.
The course was held from September 9th to September 10th 2021, and the PhD student was introduced to several databases containing climatic, topographic, and anthropogenic variables. She learned how to download raster variables, extract pixel values, convert categorical variables to a continuous form, and how to adjust the spatial range and resolution of different rasters. The practical part

of the course was conducted in the R Studio environment.

Dianthus ciliatus s.l. populations

Populations of Dianthus ciliatus s.l. in NP Kornati

Populations of Dianthus ciliatus s.l. in NP Kornati

Through July and August, Professor Dr Sandro Bogdanović, project collaborator, collected 17 populations of Dianthus ciliatus s.l., one population of Dianthus sylvestris and two populations of the genus Aurinia.
Populations were collected in Dalmatia, Istria, Albania and Montenegro.

Populations of Dianthus ciliatus ssp. dalmaticus, Kozjak

Populations of Dianthus ciliatus ssp. medunensis, Albania, Kruje

Field research in the Alps

From 1st to 5th of August 2021, external project associate, Dr Božo Frajman (assistant professor at the Institute of Botany, University of Innsbruck) and PhD student Marko Doboš collected samples of the genus Festuca in the Italian and Austrian Alps.

 

Fieldtrip started in the beautiful Italian Dolomites, in the area of Seiser Alm (Alpe di Siusi) in the Sciliar-Catinaccio Nature Park, and the same day we sampled in the border area of Austria and Italy, in the massif known as Villgratner Berge (Defreggengebirge) above the village of Kalkstein in Austria. 

 

The next day we sampled around the Turracher Höhe mountain passes in the Gurktaler Alpen massif and the Sölk Pass in the Niedere Tauern massif. The slightly more demanding Ennstaler Alpen, ie the top of Hochtor, came the next day, and then we collected related species that grow at relatively lower altitudes, east of the village of Admont, above the river Enns on the slopes of the Kalkalpen and around Lake Leopoldsteiner See. on the Seemauer ridge, which is part of the Hochschwab Alps.

Field research in the Balkans

During July, it was time for fieldtrips on the Balkans and collection of research material. From 15th to 26th of July 2021 we travelled thousands of miles across the Balkans in search of plants from the genera Festuca, Dianthus and Aurinia. The fieldtrip was done by the project leader Dr Ivana Rešetnik, project associate Associate Professor Dr Ivica Ljubičić and PhD student Marko Doboš.

We started sampling in Bulgaria where we climbed to the highest peak of the Pirin, Vihren, and the next day we were already on the highest peak of the Slavyanka mountains, Gotzev, in the Ali Botush area located on the Bulgarian-Greek border.

 

 We crossed into Greece and sampled on the Vrontous and Menikion mountains the same day, and the next day we climbed Dudica (Visogrand) on the Greek-Macedonian border where we were caught in a storm but we still managed to sample. Then came Kajmakčalan (Nidže), also on the Greek-Macedonian border, and then we crossed into Macedonia where we were on Mount Bistra and the top of Kobilica on Shar Mountain. The next place we sampled is the Mali me Gropa area in Albania, east of Tirana, whose unreal landscape resembles the surface of the moon.


After that, we headed north towards Prokletije, into the canyon of the river Valbona, followed by a long drive along winding roads to Shkodra. In Montenegro, we sampled along the roads, and the next day we were on Hrgud and Mount Velež in Bosnia and Herzegovina.

We collected a total of 14 new populations of the genus Festuca and 12 new populations of the genus Dianthus.
Beautiful mountain landscapes, amazing species and wonderful people we met along the way made this demanding field sampling an unforgettable experience!

PhD student Ana Terlević and project associate Ivica Ljubičić collected samples of Dianthus sylvestris leaves for molecular analyzes at the top of Klečica near Ogulin on June 16,2021.

 

Field research in italy

From 28.6.2021 to 11.7.2021. project leader Dr Ivana Rešetnik, project associates Dr Sandro Bogdanović and Dr Martina Temunović, and doctoral student Ana Terlević were on a field research in Italy. The purpose of the field research was to collect individuals from the genus Festuca and the genus Dianthus. We bring a short report of field research accompanied by a road map and photographs of field work and plant taxa recorded in the field:
We visited 6 national parks (Gran Sasso & Monti della Laga National Park and Maiella National Park in the province of Abruzzo, Gargano National Park in the province of Puglia, Cilento & Vallo di Diano National Park in the province of Campania, Appennino Lucano National Park - Val d'Agri - Lagonegrese and Pollino National Park in the province of Basilicata);

We climbed 10 mountain peaks (Monte Velino, Monte Porrara and Monte Rotella in the province of Abruzzo, Monte Cotento in the province of Lazio, Monte Cervialto and Monte Cervati in the province of Campania, Monte Sirino, Serra del Prete, Monte Pollino and Serra Dolcedorme in the province of Basilicata);

We toured habitats ranging from 3 to 2139 m above sea level; we traversed pastures, rocks, and forests;

 

In total, we collected about 90 individuals of the genus Festuca and about 190 individuals of the genus Dianthus, and along the way we enjoyed the flora of Italy and the company of horses and cows on mountain pastures.

  

From June 28 to July 1, 2021, postdoctoral fellow dr.sc. Maja Mucko participated in the online course "Programming in Python (D460)". The course was organized by the University of Zagreb, University Computing Center Srce. The course deals with advanced structural and object-oriented programming functions, sorting algorithms and design patterns.
The course lasted a total of 4 days of 4 school hours. Attendees learned to create simple programs using the listed functions, algorithms and patterns.

More about the course at the link: https://lms3.srce.hr/moodle/course/view.php?id=175

From 23 to 25 June 2021, doctoral student Ana Terlević, postdoctoral fellow dr.sc. Maja Mucko, project associate dr.sc. Martina Temunović and project leader dr.sc. Ivana Rešetnik participated in the online course "Using the computer cluster Isabella". The course was organized by the University of Zagreb, University Computing Center-Srce. The course covers the basic functions, commands, modules, packages and working with files within the HTC Cloud cluster identical to the computer cluster Isabella, available to the academic community. The course lasted a total of 2 days of 4 school hours with 3rd additional day for Q&A. Participants learned to access the cluster, set up jobs and manage jobs on the cluster.

More about the course at the link: https://lms3.srce.hr/moodle/course/view.php?id=187

From June 8 to 11, 2021, postdoctoral student Maja Mucko participated in the online course "Fundamentals of Programming (Python) - webinar (D450)". The course was organized by the University of Zagreb, Computing Center Srce. The course covers basic functions, commands, modules, packages and files managing within the basic framework of structural programming with the Python programming language. The course lasted a total of 4 days of 4 school hours, and the participants learned the logic of programming in Python through example problem solving.

More about the course at the link: https://lms3.srce.hr/moodle/login/index.php

PhD student Ana Terlević attended the on-line ForBio course “Introduction to Bioinformatics”, held from April 26 to 30, 2021.
This course was organized by Research School in Biosystematics – ForBio. Course covered following topics: introduction to UNIX and the command line, best practices for using Saga - the Norwegian academic HPC system, introduction to various dana formats for biological analyses (FASTA, FASTQ, SAM, BAM, VCF), development of workflow for assembling plastid data and performing BLAST alignments, phylogenetic analysis, as well as using R/R-studio for data management and visualization. Course link: https://www.forbio.uio.no/events/courses/2021/bioinfo_intro_2021.html

 

Zoom lecture. Lecturer José Cerca.

Solving exercises in the command line (Ubuntu).

The tenth project meeting

The tenth project meeting was held 08/04/2021, at the Department of Agricultural Botany, Faculty of Agriculture (Svetošimunska street 25). The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Maja Mucko, Ana Terlević, Marko Doboš and project associates Sandro Bogdanović and Martina Temunović and Božo Frajman.

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Postdoctoral fellow Maja Mucko, PhD hired

On April 6th, 2021, postdoctoral fellow Maja Mucko, PhD, joined the project. Maja will conduct analyses related to population genetics and phylogeny of Festuca bosniaca, i.e. the group Festuca varia.
Welcome! 

Ivana Rešetnik at the course "Morphological phylogenetics: principles, applications, and techniques" From January 15th to 26th, 2021, Ivana Rešetnik attended the course "Morphological phylogenetics: principles, applications, and techniques".

Ivica Ljubičić at the course "Species Distribution Modeling using R"

Ivica Ljubičić in the period 25-29 January 2021 participated in the scientific workshop "Species Distribution Modeling using R", which was attended by about 20 members of various scientific and educational institutions from all over the world..

 

Ivana Rešetnik at the course "Introduction to Python for Biology "

From January 11th to 15th, 2021, Ivana Rešetnik attended the course "Introduction to Python for Biology".

 

Ninth project meeting held

The ninth project meeting was held 01/21/2021, at the Department of Agricultural Botany, Faculty of Agriculture (Svetošimunska street 25). The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Ana Terlević, Marko Doboš, and project associates Sandro Bogdanović and Martina Temunović.

Work activities of PhD student Marko Doboš

Preparation of samples of the genus Festuca for DNA isolation in a Molecular laboratory for plant systematics in Zagreb. 

 

Staining of Festuca leaf sections and making permanent preparations - (left image).
Photographing microscopic preparations of Festuca bosniaca specimens - (image right).

Work activities of PhD student Ana Terlević

 

Morphometric measurements of Dianthus sylvestris samples

 

Germination of seeds of the genus Dianthus.

Postdoc position on the project – announcement

On 12/30/2020, a call for postdoctoral candidates II on the project was announced on the Faculty of Science website, Official Gazette (https://narodne-novine.nn.hr/clanci/oglasi/o8309621.html) and the EURAXESS portal. Candidates must meet the requirement: PhD in natural sciences (biological / biochemical) or related sciences (biotechnical), and desirable additional skills are: excellent command of written and spoken English. Preference will be given to applicants with experience in (one or more of the following areas): scientific research in botany, working in a molecular laboratory, computer analysis of genomic data and / or in general large-scale data processing / bioinformatics. Practical experience in spatial analysis, GIS, methods of ecological niche modeling, and R is also desirable.
The process of releasing the Expert Committee report for comment to competitive applicants is currently underway.

Internal project workshop "Introduction to the programming language R"

Postdoctoral fellow Marin Grgurev held an internal project course "Introduction to the programming language R" from 14-17 of December 2020, attended by members of the project team Ivana Rešetnik, Ivica Ljubičić and Marko Doboš.

 

 

PhD student Marko Doboš at the University of Innsbruck, Austria

PhD student Marko Doboš spent two weeks (26 October - 8 November 2020) at the University of Innsbruck, Department of Botany, as part of the Evolutionary Systematics research group led by Prof. Peter Schöenswetter, where he measured the relative genome size of samples of the species Festuca bosniaca using flow cytometry.

Relative genome size (RGS) measurement and degree of ploidy on a flow cytometer.

Eighth project meeting held

The eighth project meeting was held 10/16/2020, at the Department of Botany, Faculty of Science (Marulić square 20/2). The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Marin Grgurev, Ana Terlević, Marko Doboš, and project associates Sandro Bogdanović and Martina Temunović.

Project leader Ivana Rešetnik at the Institute of Botany (Prague, Czech Republic)

Project leader Ivana Rešetnik was in Prague from 05.10. to 11.10.2020 at the Institute of Botany, Czech Academy of Sciences, with dr.sc. Eliška Zaveska. During this time the genus Aurinia data gained and analysed so far were discussed and additional analyses were carried out.

  

Project proposal submitted

A project entitled "Digitization of Dianthus Collections" was written by PhD student Ana Terlević and submitted to the SYNTHESYS + Virtual Access competition. The project was written in collaboration with the curators of the collections WU (Natural History Museum Wien), BP (Hungarian Natural History Museum), PR (National Museum Prague), K (Royal Botanic Gardens Kew), BR (Meise Botanic Garden), Hebrew University Jerusalem and E (Royal Botanic Gardens Edinburgh), as well as colleagues from the University of Berlin (Prof. Dr. Thomas Borsch), the University of Heidelberg (Prof. Marcus Koch), the University of Pisa (Assoc. Prof. Dr. Lorenzo Peruzzi) and the University of Zürich (Prof. Dr. Alex Widmer).
The project involves the digitization and public accessibility of the entire genus Dianthus in these collections, which are among the largest and most important herbarium collections in Europe and have been selected for funding.
 

Seventh project meeting held

The seventh project meeting was held 09/11/2020, at the Department of Botany, Faculty of Science (Marulić square 20/2). The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Marin Grgurev, Ana Terlević, Marko Doboš, and project associate Sandro Bogdanović.

Field research of the genus Festuca

Samples of the genus Festuca were collected during a three-day field research (21-23 of July 2020) at the Crnopac, Kamešnica and Kremen sites. A one-day field trip to Vlašić (Bosnia and Herzegovina) was also conducted.

  

All collected herbarium specimens were processed so that they were all arranged in labelled folders.
Herbarium speciments (vouchers) are kept in the collection Herbarium Croaticum (ZA).

Herbarium vouchers of individuals of the genus Festuca sorted into herbarium with the corresponding label.

Sixth project meeting held

The sixth project meeting was held 06/24/2020, at the Department of Botany, Faculty of Science (Marulić square 20/2). The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Marin Grgurev, Ana Terlević, Marko Doboš, and project associates Sandro Bogdanović and Martina Temunović.

Field research of the genus Dianthus in Istria

Due to the SARS-CoV-2 pandemic, it was not possible to carry out the planned field research abroad (Italy, Slovenia, Bulgaria). The growing season of the second project year was used for additional field research in Croatia, where possible.
Samples of the genus Dianthus were collected in Istria at three one-day sites.
The sites included Lim Bay (21 of June 2020), Ćićarija and Plomin (19 of July 2020).

Ana Terlević at ETH Zürich, Switzerland

In March 2020, PhD student Ana Terlević visited ETH Zürich as part of the Department of Environmental Systems Science under the supervision of Prof. Alexa Widmera. Due to the SARS-CoV-2 pandemic, her stay was shortened by 10 days.

Preparation of Dianthus samples for DNA isolation and preparation of the NGS library (ETH Zürich).

Zagreb earthquake

The earthquake that struck Zagreb on March 22, 2020 caused severe damage to all the buildings of the Department of Biology at the Faculty of Sciences in Zagreb. The buildings where most of the activities related to the work on this project are carried out are located in the center of Zagreb at the addresses Marulićev Square 20 and Marulićev Square 9a. Considering the fact that the other laboratories of the Department of Biology were in a similar condition, it was not possible to carry out several project work tasks. 


The damage to the Molecular Laboratory for Systematic Botany at Marulićev Square 9a.
The second part of the project team is located at the Department of Agricultural Botany within Pavilion I of the Faculty of Agriculture at Svetošimunska street 25 in Zagreb, which is relatively close to the epicenter of the Markuševac quake.

The damage of Pavilion I of the Faculty of Agriculture at Svetošimunska street 25.

Internal project workshop "Introduction to QGIS"

From February 18th to 21st, 2020, postdoc Marin Grgurev held an internal project workshop "Introduction to QGIS" for members of the project team. The workshop covered topics related to the preparation, processing and analysis of spatial data using QGIS open source software.

 

PhD student Marko Doboš visits herbarium collections Z and ZT

From February 10th to 14th, 2020, PhD student Marko Doboš was at the Universität Zurich, Switzerland, where he visited the herbarium collections Z and ZT. During his visit, he examined herbarium specimens of the genus Festuca species from the Varia group.

  

PhD student Ana Terlević at the course "Fundamentals of Programming in R"

From February 10th to 12th, 2020, PhD student Ana Terlević attended the course "Fundamentals of Programming in R (S760)" organized by the University Computing Centre in Zagreb.

Postdoctoral fellow Marin Grgurev at the course "Advanced Linux System Administration II"

From December 9th to 13th, 2019, Marin Grgurev attended the “Advanced Linux System Administration II (L220)” course organized by the University Computing Centre in Zagreb.

Postdoctoral fellow Marin Grgurev at the course "Advanced Linux System Administration I"

From November 11th to 15th, 2019, Marin Grgurev attended the “Advanced Linux System Administration I (L210)” course organized by the University Computing Centre in Zagreb.

PhD student Marko Doboš at the Institute of Botany (Belgrade, Serbia)

From November 4th to 11th, 2019, PhD student Marko Doboš visited the Institute of Botany in Belgrade, Serbia, where he perfected techniques for anatomical preparation of leaf cross sections and morphometric analyses of genus Festuca species under the guidance of prof. Dmitar Lakusic and Nevena Kuzmanović, PhD. A detailed protocol for was developed as the result of the visit.

Preparation and staining of leaf cross sections (left) and preparation of habitus and inflorescence morphometry (right).

  

Leaf cross section of Festuca bosniaca after staining. 

Training at the University of Innsbruck, Austria

During November 2019, project leader Ivana Rešetnik and PhD student Ana Terlević received training at the University of Innsbruck, Department of Botany, Research Group Evolutionary Systematics. Ivana Rešetnik prepared an NGS trial library on selected species of the genus Aurinia. Ana Terlević measured the relative genome size of Dianthus sylvestris and Festuca bosniaca samples collected during 2018 and 2019.

   

 

Determination of relative genome size of Dianthus sylvestris samples

 

Determining the relative genome size on a Partec CyFlow Space flow cytometer

Fifth project meeting held

The fifth project meeting was held on October 11th 2019, at the Department of Botany, Faculty of Science. The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Marin Grgurev, Ana Terlević, Marko Doboš, and project associates Sandro Bogdanović and Martina Temunović.

Postdoctoral fellow Marin Grgurev at the course "Linux System Administration II"

From October 14th to 18th, 2019, Marin Grgurev attended the “Linux System Administration II (L120)” course organized by the University Computing Centre in Zagreb.

The search for nomenclature types

Festuca bosniaca is a complex species that, at its edges of distribution, vaguely transforms into other closely related species. One of the project goals is to investigate its delineation and to potentially determine if related taxa truly deserve species status. This requires exploration of first descriptions, synonymy and taxonomy of F. bosniaca and related species from the Varia group.
 

 

The first description of Festuca bosniaca in Kummer, F., Sendtner, O. (1849): Enumeratio plantarum in itinere Sendtneriano in Bosnia lectarum, cum definitionibus etc. Sectio secunda. Flora (Regensb.) 32: 756.

Postdoctoral fellow Marin Grgurev at the course "Linux System Administration I"

From September 16th to 20th, 2019, Marin Grgurev attended the “Linux System Administration I (L110)” course organized by the University Computing Centre in Zagreb.

PhD student Ana Terlević at the course "The syntax of the R language"

From September 16th to 20th, 2019, PhD student Ana Terlević attended the course "Introduction to R syntax and its application in basic statistical and graphical data analysis (S720)" organized by the University Computing Centre in Zagreb.

PhD student Marko Doboš hired

From September 16th, 2019, Marko Doboš mag. oecol. et prot. nat. is employed on the project through the Croatian Science Foundation call "Career Development Project for Young Researchers - Training of New Doctors of Science" DOK-09-2018. Marko will be researching the morphological and genetic diversity of Festuca bosniaca for his PhD thesis. Welcome Marko 

Marin Grgurev and Ana Terlević at “4th International Summer School on Data Science” Summer School

From September 9th to 13th, 2019, Marin Grgurev and Ana Terlević attended the “4th International Summer School on Data Science” Summer School in Split, where simple and complex statistical concepts (ANOVA, regression, PCA, symbolic data analysis, etc.) were processed as part of lectures and software practicum.

Fourth project meeting held

The fourth project meeting was held on September 4th 2019, at the Department of Botany, Faculty of Agriculture. The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, and project associates Sandro Bogdanović and Martina Temunović.

 

Postdoctoral fellow Marin Grgurev at the workshop "Using an Isabella computer cluster"

On September 4th, 2019, Marin Grgurev attended the “Using an Isabella computer cluster” workshop organized by the University Computing Centre in Zagreb.

Fourth field collecting trip finished

Fourth field research was conducted in two separate groups. From July 9th to 11th, 2019, Ivica Ljubičić and Ana Terlević did the research in Slovenia, while from July 9th to 21st, 2019, Ivana Rešetnik, Marin Grgurev, Marko Doboš and Sandro Bogdanović were collecting the Aurinia, Festuca and Dianthus specimens in Northern Macedonia, Greece and Serbia.

 

Field research – Slovenia a) Dianthus sylvestris, b) mountain trail Topol-Grmada-Tošč, SLO 11. 7. 2019.

 

 

 

 

 

Field research – phase 4: a) Kopaonik, SRB 10.07.2019 D170 Dianthus sylvestris, b) Kopaonik, SRB 10.07.2019, c) Korab, MKD 13.07.2019 Fb054 Festuca bosniaca, d) Korab, MKD 13.07.2019 D175 Dianthus sylvestris, e) Korab, MKD 13.07.2019, f) Kajmakčalan, GR, 13.07.2019

Third field collecting trip finished

Ivana Rešetnik, Ivica Ljubičić, Sandro Bogdanović and Ana Terlević conducted the field research in Greece, Albania nad Montenegro from June 19th to 30th, 2019.

 

 

 

 

Field research – phase 3: a) Pindus Mts GR 21.06.2019, b) Gorilla (Kourila) Mt. GR 22.06.2019_D132 Dianthus sylvestris subsp. alboroseus, c) Bjeshkët e Nemuna, Thethi AL 28.06.2019_D36 Festuca sp., d) Tymfi Mt., GR, 23.06.2019

Postdoctoral fellow Marin Grgurev at the course "Radar and optical Remote Sensing in the Agricultural and Environmental Monitoring "

From June 20th to 24th, 2019, Marin Grgurev attended the "Trans-Atlantic Training 2019: Radar and Optical Remote Sensing in Agricultural and Environmental Monitoring" course hosted by NASA's Land-Cover / Land-Use Change Program, European Space Agency and SCERIN, held in Novi Sad, Serbia.

 

2019 field research started 

Field research for 2019 began with a three-day excursion from June 4th to 6th, 2019, with sample collecting on Mosor, Brač, Lastovo, Poštak and Klek.

 

  

 

Ivana Rešetnik at “Phylogenomics” Workshop

From May 20th to 25th, 2019, project leader Ivana Rešetnik attended the "Phylogenomics" workshop in Berlin (Germany). The workshop covered topics related to phylogenetic analyses of genomic data.

 

Postdoctoral fellow Marin Grgurev hired

On April 15th, 2019, postdoctoral fellow Marin Grgurev, PhD, joined the project. Marin will conduct analyses related to the development of ecological niche models for the past and present.
Welcome Marin!

Third project meeting held

Third project meeting was held on September 4th, 2019, at the Department of Botany, Faculty of Agriculture. The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Marin Grgurev, ana Terlević and project associates Sandro Bogdanović and Martina Temunović.

PhD position on the project – announcement

On the webpage of the Faculty of Science, in the Official Gazette and on the EURAXESS portal, an open call for the PhD position on the project was published on 13.03.2019. The doctoral candidate will be primarily involved in the phylogeography of the species Festuca bosniaca. The doctoral thesis will include morphological, molecular and taxonomic-nomenclature research - i.e. field sampling, herbarium specimens sampling, morphometry, and work in a molecular laboratory. Participation in practical teaching at the Department of Botany is also expected. Positive and enthusiastic work attitude, willingness to work intensively and participate and present work results at various events, as well as readiness to attend workshops and courses in the HR and abroad are expected from the candidates.

RADseq workshop in Innsbruck, Austria

Between 25.02. and 02.03.2019. Ivana Rešetnik participated at the RADseq workshop, which was organized at the University of Innsbruck, Department of Botany, within the Research Group Evolutionary Systematics of Peter Schönswetter, Mag. Dr. Prof. Workshop was held by Eliška Záveská PhD and Filip Kolář PhD.

 

Working space adaptation

Adaptation and modification of several rooms were made at Marulić Square 20/II, where most of the members of the research team will be working. The adaptation provided a working space for doctoral and postdoctoral team members. A part of the laboratory where the fixing of materials for morphometric measurements will be carried out was also renovated.

 


Postdoc position on the project – announcement

On the Faculty of Science webpage, in the Official Gazette and on the EURAXESS portal the open call for the Postdoc position on the project was published on 04.01.2019. Applicants had to fulfil the mandatory requirement of holding a PhD degree in the field of natural sciences (biological/biochemical) or related sciences (biotechnical), while the additional requirements included excellent knowledge of both oral and written English. Applicants were required to have a background in (one or more of the following areas): scientific research in botany, experience in a molecular lab, computer analysis of genomic data and/or generally in statistical processing of large amounts of data/bioinformatics. Also, it was desirable to have a practical experience in spatial analysis, GIS, ecological niche modelling methods and R.

The search for nomenclature types

The quest for nomenclature types commenced with a survey of old literature in which the names and synonyms of the investigated taxa were first published.
The first description of the species is Dianthus sylvestris Wulfen of Jacquin (1786). It is assumed that the original material according to which F. X. von Wulfen described the species D. sylvestris was destroyed during the World War II, which is why Bacchetta et al. (2010) chose the iconography in watercolours (Jacquin 1781, p. 82) as neotype.


Morphometry on the collected samples in progress

The herbarium specimens collected during the first year of project implementation were processed by placing all specimens in marked folders and all relevant location information stored in the Flora Croatica Database digital database.
Preliminary morphometric measurements were started on the collected material to initiate the procedure and drafting the protocol. The relevant characteristics are recorded according to literature data for the purpose of preparing a preliminary set of morphometric features which will be measured.

 

Isolation of DNA from collected samples in progress

In the Molecular Laboratory for Plant Systematics, at Marulić Square 9a, DNA isolation from selected preliminary set of samples collected on field began. For the isolation of the DNA, about 25 mg silica gel-dried list tissue is used for each sample, and DNA isolation is performed using a GenElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich) for isolating plant DNA.

Second project meeting held

The second project meeting was held on 11.10.2018. at the Department of Botany, Faculty of Agriculture. The meeting was attended by members of the research team: Ivana Rešetnik, Ivica Ljubičić, Ana Terlević, and project associates Sandro Bogdanović and Martina Temunović.


Second field collecting trip finished

Second field research was conducted from 10.07. to 20.07.2018 on the territory of Bosnia and Herzegovina and Montenegro. Specimens of Aurinia, Festuca and Dianthus genera were collected for genetic and morphometric analyses.

 
Dianthus bertisceus                                                         Durmitor Crna Gora_13.07.2018.

 

Plana Crna Gora_14.07.2018. Pastirska nastamba                            Prokletije Popadija Crna Gora_14.07.2018.

 

Medun Crna Gora_15.07.2018. D98                               Kanjon Morače Crna Gora_15.07.2018.
Dianthus medunensis

First field collecting trip finished

The first field research was conducted from 13.06. to 24.06.2018 and included the area of northern Italy, Slovenia, Croatia and Bosnia and Herzegovina. Specimens of Aurinia, Festuca and Dianthus genera were collected for genetic and morphometric analyses.

 

            Petrinje_SLO 13.06.                                                            Kranjski Snežnik_SLO 14.06.2018.

 

Kranjski Snežnik_SLO 14.06.2018._FB1                                       Velebit_Paklenica_17.06.2018.

Festuca bosniaca

 

Biokovo_18.06.2018_D47 Dianthus sp.


PhD position on the project – announcement

On the Faculty of Science webpage, in the Official Gazette and on the EURAXESS portal an open call for the PhD position on the project was published on 16.05.2018. The doctoral candidate will be primarily involved in the phylogeography of the Dianthus sylvestris group. The doctoral thesis will include morphological, molecular and taxonomic-nomenclature research: i.e. field sampling, herbarium specimens sampling, morphometry, and work in a molecular laboratory. Participation in practical teaching at the Department of Botany is also expected. Positive and enthusiastic work attitude, willingness to work intensively and to participate and present work results at various events, as well as readiness to attend workshops and courses in the HR and abroad are expected from the candidates.

Kick-off meeting held

The project kick-off meeting was held on 11.04.2018 at the Department of Botany, Faculty of Agriculture. The meeting was attended by members of the research team: Ivana Rešetnik and Ivica Ljubičić, and project associates Sandro Bogdanović and Martina Temunović.