GAbridge
Fund: Croatian Science Foundation
Project type: Research project
Project Code: IP-2022-10-8926
Project title: Bridging the Disciplinary Gap: Integrating Animal Genetics and Archaeology in Croatia.
Total requested grant from HRZZ (EUR): 198.888,39.
Project duration: 20.12.2023. to 19.12.2027.
Institution in which the project is carried out:
University of Zagreb Faculty of Agriculture
Prof. Ivica Kisić, PhD
Svetošimunska cesta 25, 10000 Zagreb, Croatia
Phone: +385 1 239 3779
Fax: +385 1 231 5300
E-mail: dekanat@agr.hr
Project Manager:
University of Zagreb Faculty of Agriculture
Department of Animal Science
Laboratory for Archaeogenetics
Prof. Vlatka Čubrić Čurik, PhD
Phone: +385 1 239 4008
E-mail: vcubric@agr.hr
Associates from the Faculty of Agriculture:
Prof. Ino Čurik, PhD.H
Prof. Neven Antunac, PhD
Assist. Prof. Vladimir Brajković, PhD
Ivana Držaić, PhD
Assoc. Prof. Maja Ferenčaković, PhD
External associate:
Dinko Novosel, PhD, Veterinary Institute, Zagreb, Croatia
Strahil Ristov, PhD, Ruđer Bošković Institute in Zagreb
Assoc. Prof. Rajna Šošić Klindžić, PhD, University of Zagreb, Faculty of Humanities and Social Sciences
Maja Grgurić Srzentić, University of Zadar
Maja Krznarić Škrivanko, City museum Vinkovci
Goran Tomac, University of Zagreb, Faculty of Humanities and Social Sciences
Summary
The Mendthegap project was an innovative way to fill the gaps in the research capacity on the past in Croatia in the fields of archeology and genetics and to bring these two disciplines closer together. The sustainability of the Mendthegap project began with research capacity building, i.e. with the establishment of the Laboratory of Archaeogenetics at the Faculty of Agriculture, where archaeogenetic analyzes can be carried out. As the latent scientific potential has been tapped in the Republic of Croatia, the GAbridge project would provide direct scientific results on the origin and past of cattle in the Republic of Croatia. Next generation sequencing (NGS) methods and data processing capabilities have opened a wide range of new opportunities in various scientific fields. Here we have gathered experts in molecular genetics, population genomics, animal breeding, informatics, and archeology to answer various questions related to population genomics and biodiversity (mixing and population structure) and the distribution of cattle in our region as the most important domestic animal for the development of mankind. By analyzing ancient cattle bones (> 12,000) years, we would improve our understanding of genomic changes in the process of domestication. Our project proposal includes a strong component of theoretical power to estimate genetic introgression, effective population size, and individual admixture. In addition, NGS will be performed on old cattle with the following objectives: (i) determine the genetic diversity of ruminants in the Paleolithic: understand the genetics of predomestication, (ii) contribute to the understanding of the domestication process during the Neolithic in Croatia, (iii) clarify the chronology of cattle distribution: (iv) investigate the genetic origin of Croatian cattle breeds, and (v) bridge the disciplinary gap and establish a long-term collaboration between archeologists and geneticists to decipher the past.
Theoretical background and the scientific contribution of the project
Archaeogenetics is a young and respected scientific discipline that is rapidly developing with the advent of next generation sequencing (NGS), and the results of its research are frequently published in the most prestigious journals. Croatia is known for its numerous archaeological sites and wealth of archaeological material of biological origin (animal and human bones), the analyses of which have enriched our knowledge of the human past. A good example of this is the Neanderthal bones from Vindia. We started in 2016 with the competition H2020-TWINN-2015: Spreading excellence and cooperation" and won the first place out of 535 submitted projects and launched the project MendtheGap - Smart integration of genetics with the sciences of the past in Croatia: noticing and bridging the gap. This project was designed to overcome and repair all current "gaps" and enable the smart use of existing opportunities by strengthening the research activities of the science of the past in Croatia and beyond, as there is no similar group in the region. The construction and establishment of a laboratory for archaeogenetics creates conditions for scientific excellence in the field of archaeogenetics in the region, which makes us an attractive, sought-after partner in future applications for EU scientific projects, which is in line with the smart specialization strategy of the Republic of Croatia. In general, training for work in archaeogenetics represents a demonstration of knowledge and skills and is a proof of scientific excellence that elevates training in other disciplines of applied genetics (human and veterinary medicine, agriculture and forestry, biology, etc.) to a higher level. We started in 2016 with the H2020-TWINN-2015 competition and Mendthegap and continued our work through the laboratory construction project to maintain this interdisciplinary idea. With the intention of conducting cutting-edge scientific research and establishing scientific collaboration between geneticists and scientists who study the past (archaeologists, geologists, biologists, etc.), the goal of this project is precisely to decipher the past of cattle before and after domestication in our region through an interdisciplinary and holistic approach, which will bring many new insights and archaeological research on these eras.
Methodology
Bridging the disciplinary gap: the integration of animal genetics and archeology in Croatia will take place in 6 separate work packages (WPs) representing large units with one or several objectives:
- WP1. Genetic diversity of cattle in Palaeolithic: understanding of predomestication genetics
Leader: Vlatka Čubrić Čurik
Co-leader: Maja Krznarić Škrivanko
Supervision: Preston Miracle
Associates participating in the package: Ino Čurik, Ivana Držaić, Vladimir Brajković, PhD student
Croatia is known for its rich zooarchaeological remains (mainly bones) of animals (Miracle and Brajković, 1992; Miracle et al., 2010; Lenardić et al., 2017) from different stages of the domestication process (before domestication, in the early and later stages of domestication). The analysis within the Archaegenetics project will contribute to a better understanding of the domestication process, especially when Croatia is located on the main migration routes from the Middle East to Europe (Zilihao 2001; Beja-Pereira et al., 2006). There are two competing hypotheses, one supporting the migration of domesticated animals including interbreeding of domestic and wild animals (Loftus et al., 1999; Cymbrion et al., 2005) and the other supporting the complexity of the domestication process including inbreeding of domestic and wild animals (Beja-Pereira et al., 2006). Thus, when considering the domestication of cattle, we expect to find traces of the mitogenome of the ancient aurochs population that once lived in our area. In this work package, aDNA will be extracted mainly from aurochs and cattle prior to the domestication processes, and a distinguished zooarchaeologist from St. Johns of the University of Cambridge. We also expect considerable help with this project from our museologists. Extraction of aDNA from the first 100 samples will be performed using the classical phenol-chloroform method with prior physical purification of the samples. Special attention will be paid to contamination. It will be started with 50 samples, from which we hope to have successfully isolated 20 to 30 aDNA. Using the "capture enrichment method" (Maricic et al. 2010), the mtDNA library will be prepared for NGS sequencing. From 20-30 aDNA, we expect at least 15 libraries to have 5-10 whole mitogenomes after NGS sequencing. The sequences obtained will be compared with sequences from genetic repositories using various software, such as Clustal Omega (Sievers et al., 2011), MEGA 7 (Kumar et al., 2016), Network version 5.0.0.3. (Bandelt et al., 1999), PopArt (Leigh and Bryant 2015), Galaxy platform (Afgan et al., 2016), Mitotoolpy (Peng et al., 2015), and SAS software version 9.3 (SAS Institute, Cary, North Carolina, USA). A large database of mitogenomes is being compiled. BEAST 2 (Bouckaert et al., 2014), a program for Bayesian phylogenetic analyzes (Rieux and Khatchikian 2017), is used. The program estimates rooting (Duchêne et al., 2011), (Rieux and Khatchikian 2017) time-scaled phylogeny using "strict" or "relaxed" molecular clock models. BEAST2 uses a Markov chain Monte Carlo (MCMC) method such that each tree is proportionally determined by its posterior probability.
- WP2. Understanding domestication process during neolithization: evidence from ancient DNA
Leader: Ivana Držaić
Co-leader: Rajna Šoštarić
Supervision: Hrvoje Vulić, Preston Miracle, Johann Soelkner
Associates participating in the package: Ino Čurik, Vladimir Brajković, Maja Grgurić Srzentić, Maja Ferenčaković, Neven Antunac, PhD student
In this work package, unlike previous extractions, most of the extraction of aDNA will occur after the domestication processes. We will be assisted in sample selection by our colleague Hrvoje Vulić for the Neolithic and by our colleague Johann Soelkner for the Adametz collection, which represents cattle from the last 100-200 years, when the breeds originated. We also expect significant help from our museologists on this project. This work package will use the same aDNA extraction methodology as the historical DNA (Adametz collection) (100 samples total), using the classic phenol-chloroform method as in the previously described package. The analyzes will be performed in the Archaeogenetics Laboratory of the Faculty of Agriculture. In addition, as previously described, the capture enrichment method and whole genome sequencing will be used. Accordingly, bioinformatics analyzes will also be performed.
- WP3. Ancestral Recombination Graphs: resolving chronology
Leader: Dinko Novosel and co-leader: Maja Ferenčaković
Supervision: Gregor Gorjanc
Associates participating in the package: Ino Čurik, Vladimir Brajković, Stasa Ristov, PhD student, postdoctoral student
In this package, the use of Ancestral Recombination Graphs is introduced (ARG) as a common genetic platform between animal genetics and archaeology is presented. Colleague Gregor Gorjanc has recently started to develop research in this area. It is important for breeding plans in distantly related populations. Namely, in animal breeding we have several breeds with different degrees of genetic relatedness due to populations with common ancestors. These populations are the ancestors of today's animal breedsthat lived at different times in the past, and ancestral recombination diagrams are the ideal concept to connect all these populations. Ancestral recombination diagrams are also a key object in population genetics as well as in archaeogenetics, which is growing rapidly. Since ancestral recombination graphs are key to future research in both fields, using simulated and real data on whole genome sequences, we will be able to make inferences about genetic connectivity between samples over time via the path of ancestral recombination graphs - current and ancient samples.
- WP4. Analysis of historical Croatian ruminant samples
Leader: Vladimir Brajković
Co-leader: Ino Čurik
Supervision: Johann Soelkner, Gregor Gorjanc
Associates participating in the package: Vlatka Čubrić Čurik, Vladimir Brajković, , Maja Ferenčaković, Ivana Držaić, Neven Antunac, PhD student, postdoctoral student
In this work package, the sequences for Croatian autochthonous cattle breeds from the Vienna Adametz collection are analyzed. The total number will depend on the success of the extracted DNA. Existing genomic databases of modern cattle created by colleague Gregor Gorjanc from Roslin Inst, Edinburgh, will be used. The sequences obtained will be analyzed for characteristic parts of the genome and SNPs and effectively used for: (i) in the assessment of population conservation status, i.e., in the assessment of inbreeding level (Ferenčaković et al., 2013 a,b, Čurik et al., 2014), different effective population sizes (Santiago et al., 2020; Mészáros et al., 2015; Rodríguez-Ramilo et al., 2015; Wang, 2016), genetic diversity (Gautier et al., 2010; Kijas et al., 2014), (ii) in determining the specificities of population structure (Decker et al., 2014) and interference (Frkonja et al., 2012; Khayatzadeh et al., 2016), and (iii) in determining the genomic regions responsible for adaptation ( Sabeti et al., 2002; Qanbari et al., 2012; Utsunomiya et al., 2012). The evaluation of all these genomic parameters is important in selected populations because it provides a reference that is a prerequisite for future biodiversity management. Special attention in the analysis of samples will be paid to the comparison of modern Croatian breeds with genotypes of samples from the past (Paleolithic, Neolithic, historical samples).
- WP5. Integration of animal genetics with archaeological evidence
Leader: Rajna Šošić Klindžić
Co-leader: Ino Čurik
Supervision: Preston Miracle, Hrvoje Vulić
Associates participating in the package: Vlatka Čubrić Čurik, Vladimir Brajković, Maja Ferenčaković, Ivana Držaić, Neven Antunac, Goran Tomac, Maja Grgurić Srzentić, Maja Krznarić Škrivanko, PhD student, postdoctoral student
In this project, we assembled a MIT disciplinary (Stock and Burton, 2011) team of Croatian scientists with expertise in molecular genetics (Vlatka Čubrić Čurik, Vladimir Brajković, Ivana Držaić), population genomics, and (Ino Čurik, Maja Ferenčaković), applied animal breeding (Maja Ferenčaković, Ino Čurik, Neven Antunac, Dinko Novosel), computer science (Strahil Ristov), and archaeology (Rajna Šošić Klindžić, Goran Tomac, Maja Krznarić Škrivanko, Maja Grgurić Srzentić). While most members of the team already have experience from previous and other projects, the new PhD student and a postdoctoral fellow will be trained in NGS analyses. Advisors in the project will additionally contribute with their advice in various aspects of the project: Hrvoje Vulić ( Neolithic archaeology), Preston Miracle (zooarchaeology), Johann Soelkner (population genetics), and Gregor Gorjanc ( quantitative genetics). As part of the project, there will be two workshops to introduce genetics to archaeologists and archaeology to geneticists. In this way, we will bring the two disciplines closer and create new value based on the concrete evidence of our sequenced cattle, putting all this in an archaeological context and helping to decipher the past of cattle in our region.
- WP6. Dissemination and management of the project
Leader: Vlatka Čubrić Čurik
Co-leader: Maja Grgurić Srzentić
Associates participating in the package: Vladimir Brajković, Maja Ferenčaković, Ivana Držaić, Neven Antunac, Goran Tomac, Maja Krznarić Škrivanko, Rajna Šošić Klindžić, PhD student, postdoctoral student
Since WP6 refers to education, dissemination and project management, they are transparent and do not need to be explained.
Project managment plan
The Gabridge project is designed as a multitransdisciplinary project involving skills and scientific research activities divided among three groups of collaborators: a) archaeologists, b) geneticists, and c) computer scientists. Collaboration with archaeologists is necessary to determine the zoo-archaeological remains of primitive cattle from sites throughout Croatia, which are located on the main migration routes from the Middle East to Europe and are of particular importance for understanding domestication processes. The vast experience of colleagues archaeologists (Rajna Šošić Klindžić, Goran Tomac, Maja Krznarić Škrivanko, Maja Grgurić Srzentić) under the supervision of Professor Preston Miracle from the University of Cambridge and consultant curator Hrvoje Vulić from the Vinkovci City Museum will enable morphological and morphometric identification of extinct primitive cattle, interpretation of results in an archaeological context, and targeted selection of samples for DNA isolation. The geneticists, Ivana Držaić, Vladimir Brajković and I, will take care of the precise extraction of a portion of the bone using the least invasive method and DNA isolation. The experience gained at the Fondazione Edmun Mach Institute, Trento, Italy under the leadership of Dr. Cristian Vernesi, then the experience of the GeoGentics Centre under the leadership of Professor Eske Willerslev, and finally the experience in our recently opened Laboratory of Archaeogenetics at the University of Zagreb, Faculty of Agriculture, will greatly help us in systematic DNA isolation under clean room conditions and library preparation for genome and mitogenome sequencing. Also, answers to the key questions of population genomics, which deals with the study of the genetic structure of populations, i.e. the analysis of the frequency of genes and genotypes in natural populations and the study of association studies to understand the genetic evolution of complex phenotypic traits in the context of quantitative genomics, will be answered by fellow geneticists Ino Čurik and Maja Ferenčaković with population genomics consultant Professor Johan Soelkner (University of Natural Resources and Life Sciences in Vienna) and quantitative genomics consultant Dr. Gregor Gorjanac (Roslin Institute, Edinburgh). Bioinformatic analysis of the genome for further population quantitative analyses requires large computer capacities, but also algorithms that accelerate and maximise the aforementioned capacities. Dr. Strahil Ristov from the Department of Electronics of the Ruđer Bošković Institute would be responsible for this part of the data processing challenge, especially with machine learning methods and deep data analysis. The management of the group is planned in coordination with the package managers and regular meetings so that analyses follows the work plan of the project. It is important to note that the coordination of the collaborators in packages WP1 and WP2 is of great importance in establishing the foundations of the project, as they relate to the selection of a bone sample, the provision of spare samples from a similar context (the trial-and-error method due to possible degraded DNA), and the process from isolation to sequencing of the archaeo-DNA that will allow further population-quantitative analyses. Special attention and regular meetings are planned for the coordination of the above packages. Dissemination of the project results will be done through active participation in international conferences and publication of scientific papers according to the planned work plan. The aim of the project is certainly the education of PhD students, postdoctoral fellows or collaborators through participation in a course and/or training at the University of Copenhagen or the University of Edinburgh, which is our strategic goal for the development of archaeogenetics in Croatia. The future analyses envisaged in this project at the recently opened Laboratory of Archaeogenetics at the University of Zagreb, Faculty of Agriculture, will require the purchase of new equipment such as Dremel grinders and certain consumables so that the analyses can be carried out according to the latest protocols. We have overlooked the necessary maintenance, servicing and upgrading of instruments such as PCR, centrifuge, workstation, but also the very important maintenance of the HVAC climate chamber and HEPA philtre, which ensure clean conditions and positive pressure (to prevent contamination) in the Laboratory of Archaeogenetics.
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