SPI-Birds Network & Database

Who we are?

The SPI-Birds Database is a searchable, publically available list of research conducted on breeding, individually marked birds across Eurasia. We host datasets on these populations and act as a central conact point for accesing the data. This is especially important for datasets that do not have sustainable data archving and data management in place. The datasets that we host are all converted into the same, standard format (see here), and thus are easier to understand and to combine. Further, we conduct quality checks on the data to correct for any mistakes in the datasets, and to warn the users about potential issues when using the data.

The associated SPI-Birds Network came together to create a community-defined, standardized method for formatting data and for describing the attributes of studied populations. In this way we greatly enhance the exchange of data, ideas, and other news within and beyond the network, as well as create equal visibility for all research groups.

We also serve as a contact point for anyone who wishes to start a new population, where we can advise on the best approach to field set-up and data management. Please use our webform to get in touch. 

Finally, and especially for students and young researchers who would like to conduct projects on long-term individually monitored bird populations, we offer an expert advice and can point you to existing open projects within our network.

Why do we do this?

Long- and short-term data on breeding birds has been collected across the globe, ranging from basic breeding and phenology data to individual data such as personality scores, genetic information, or parasite loads. Research based on these data has been of great significance for a spectrum of evolutionary and ecological disciplines. Although some collaboration has been achieved within the hole-nesting birds research community (e.g. HapMap Great tit project, ERC SHE, Pair bonds beyond breeding season), a focused, centralized, large-scale effort to establish a well-defined community working on populations of individually marked birds has been lacking. There is also no overview of existing, monitored, bird populations and their attributes (e.g. type of data collected, length of study). Furthermore, some researchers and research groups do not have a sustainable data archiving in place, which can lead to irreplacable loss of historcial information on populations.

The large number and variety of data collected (e.g. personality, nest visits) makes it difficult and time consuming to locate the populations that might fit the specific needs of potential collaborators. Even when appropriate populations are located, combining data from different populations can be a very difficult task as data formatting varies widely between different research groups. Having a uniform system for describing and storing bird data in a single, centralized location benefits both potential collaborators and database providers as it:

1. Makes it much easier for users to identify relevant populations
2. Reduces the time involved in formatting data
3. Provides a community standard of data formatting and vocabulary that can be followed by anybody establishing a new study population
4. Prevents loss of data

Become a member

The network and database membership is open to anybody who collects data on individually marked birds, including researchers or members of the general public. Anyone can use the database to search for populations of interest.

Documentation

SPI-Birds standard protocol, agreed within the community, can be found here. This document defines the standard data format. The SPI-Birds team creats tailored pipelines to convert any data format (as stored with the data owner) into a standard one.

The pipelines are available via an R package, and can be found here. 

Funding

The project is funded by NWO (Netherlands Organization for Scientific Research) grant to Dr. Antica Culina, and Centre for Biodiversity Dynamics (NTNU, Trondheim)

SPI-Birds have intially started with the hole-nesting passerines (as the most commonly studied group). We are currently expending to other bird species.

Great tit (Parus major)

The great tit has become a model species to study different ecological and evolutionary processes in the wild. These range from classical work on what determines an optimal clutch size, to more recent work on fine-scale social behaviour and social networks in wild populations. The great tit is also used as a model species to study the responses of natural populations to climate change.

Great tits are cavity nesters, but happily nest in human-made nest boxes, which enables researchers to follow their breeding behaviour. In winter, great tits usually form flocks, often with other species – recent technological advances in micro-transporders has allowed their winter behaviour and sociality to be studied. Having a wide Eurasian distribution, studying great tits also allows for comparison across populations, providing a broader understating of the drivers behind changes in natural populations exposed to different environments.

Blue tit (Cyanistes caeruleus)

Populations of blue tits are often studied alongside populations of great tits, as both species use similar type of nest-boxes for nesting. The blue tit is famous for its ultraviolet (UV-A) crest, and has been a good model organism to study the role of the UV spectrum in structural colours. While both sexes appear quite similar to humans, the UV component of the plumage (invisible to the human eye) makes them strongly sexually dimorphic to conspecifics. Studies have shown that UV is an important indicator of male quality, and that females skew the sex ratio of their offspring in response to the ultraviolet plumage ornamentation of their mates.

Blue tits are famed for their foraging skill, as they can cling to the outermost branches and hang upside down when looking for food.

Marsh tit (Poecile palustris)

Marsh tits are known to store up to several hundred food items per day, and are thus often used in studies on spatial memory in animals. To store food they use separate locations within their territory, and recover most of the stored items within 24 h. It seems that different birds have slighly different preferences for the type of sites in which they store food.

Coal tit (Periparus ater)

The coal tit is the smallest of the four tit species currently represented in our network. Like marsh tits, they hoard food - one experimental study has shown that coal tits remeber the location of the stored food as long as 4 weeks. Research has shown that hoarding behaviour varies among populations and that this likely reflects differences in competitive pressures and the prevailing environmental conditions. Furthermore, it seems that the presence of interspecific competition might reduce the effectiveness of long-term hoarding and therefore reduce winter residence.

Pied flycatcher (Ficedula hypoleuca)

Pied flycatchers are tiny long-distance migrants that winter in West Africa and breed in Europe and Western Asia. They readily accept nest boxes and are commonly used in a variety of studies, including those where experimental manipulations are applied.

During spring, male pied flycatchers have a relatively high individual variation in plumage characteristics. Base colour varies from female-brown or light grey to completely black, with intermediate shades of black and brown. They are also ornamented with a forehead patch of variable shapes and sizes and white wing patches of various sizes. The proportion of black and brown flycatchers varies widely between countries. For example, Scandinavian countries have a much higher proportion of black flycatchers than the Netherlands, where they are mostly brown.

Collared flycatcher (Ficedula albicollis)

Collared flycatchers are another model species used to study natural and sexual selection in the wild, and are also very often used to study habitat selection. The collared flycatcher is also one of the main species of wild birds used to study hybridization between species - pied and the collared flycatchers frequently hybridize in natural populations. Within their European range, the two species have two separate areas of sympatry (range overlap) where hybridization occurs. Hybrids are known to have reduced fitness. Interestingly, it has been showed that hybridization might represent adaptive mate choice under some circumstances. 

European nuthatch (Sitta europaea)

Nuthatches are long-term hoarders and can retrieve stored food up to at least 98 days after storing it. It has been shown that nuthatches use their stored seeds prudently by adjusting the amounts they ate to meet their requirements, as determined by ambient temperatures. Nuthatches refrain from using stored food during periods of relatively benign conditions so they can save the food for periods of more severe conditions.

Our network currently includes more than 60 researchers from 21 countries. To learn more about their work please follow the links provided for each name.

The network and the database are managed and coordinated by Antica Culina (NIOO-KNAW) and Marcel Visser (NIOO-KNAW).

Developement of the database pipelines is done by Liam Bailey (NIOO-KNAW) and the quality checks of database by Stefan Vriend (NTNU, Trondheim, Norway).

Members by country

Austria

• Sabine Hille, University of Natural Resources and Life Sciences Vienna

Belgium

• Erik Matthysen & Frank Adriaensen, University of Antwerp (data provided)
• Marcel Eens, University of Antwerp (data provided)

Czech Republic

• Miloš Krist, Palacky University in Olomouc (data provided)
• Peter Adamik, Palacky University in Olomouc

Estonia

• Agu Leivits, Environmental Board
• Raivo Mänd, University of Tartu (to be confirmed)

Finland

• Tapio Eeva, University of Turku (data provided)
• Markku Orell, Seppo Rytkonen & Emma Vatka, University of Oulu

France

• Anne Charmantier, Samuel Caro, Claire Doutrelant, Arnaud Grégoire, Marcel Lambrechts, Céline Teplitksy, Denis Réale, CEFE-CNR & UQAM (data provided)
• Blandine Doligez, LBBE-CNRS (to be confirmed)
• Sylvie Massemin & Josefa Bleu Institut Pluridisciplinaire Hubert Curien

Germany

• Bart Kempenaers, Max Planck Institute for Ornithology (to be confirmed)
• Michaela Hau, Max Planck Institute for Ornithology (data provided)
• Niels Dingemanse, LMU Munich (data provided)

Hungary

• János Török & Gergely Hegyi, Eötvös Loránd University (data provided)

Italy

• Camillo Cusimano, Bruno Massa & Daniela Campobello, Stazione Ornitologica, Palermo (data provided)

Ireland

• John Quinn, University College Cork (data provided)

Israel

• Aya Goldshtein, Tel Aviv University

Japan

• Teru Yuta, Yamashina Institute for Ornithology

Netherlands

• Marcel Visser, NIOO-KNAW (data provided)
• Kees van Oers, NIOO-KNAW (data provided)
• Simon Verhulst, University of Groningen
• Christiaan Both, Univeristy of Groningen

Norway

• Kjell Einar Erikstad & Tone Kristin Reiertsen, Norwegian Institute for Nature Research
• Tore Slagsvold, Oslo University
• Ole Wiggo Røstad, Norwegian University of Life Sciences

Poland

• Mariusz Cichoń & Szymon Drobniak, Jagiellonian University
• Anna Dubiec & Tomasz Mazgajski, Museum and Institute of Zoology, Polish Academy of Sciences
• Marta Szulkin, Univeristy of Warsaw
• Wojciech Kania, Polish Academy of Sciences
• Jerzy Banbura, University of Łódź (to be confirmed)

Portugal

• Ana Cláudia Norte, University of Coimbra, Portugal (data provided)

Russia

• Alexandr Artemyev, Karelian Research Center
• Anvar Kerimov, Lomonosov Moscow State University (to be confirmed)

Spain

• Juan Carlos Senar, Natural Sciences Museum Barcelona
• Jaime Potti, Estación Biológica de Doñana-CSIC (data provided)
• Alejandro Cantarero, Juan Moreno, National Museum of Natural Sciences Madrid (data provided)
• Eduardo Belda, Universitat Politècnica de València
• Emilio Barba, University of Valencia

Sweden

• Jan-Åke Nilsson, Lund University
• Caroline Isaksson, Lund University
• Lars Gustafsson, Uppsala University

Turkey

• Can Bilgin & Pinar Kavak, Middle East Technical University (to be confirmed)

UK

• Ben Sheldon & Ella Cole, EGI, University of Oxford (data provided)
• Camilla Hinde, Anglia Ruskin University
• Mark Mainwaring, Lancaster University
• Ian Hartley, Lancaster University
• Malcolm Burgess, PiedFly.Net, University of Exeter (data provided)
• Anne Goodenough, University of Gloucestershire

Projects making use of the data from multiple hole-nesting populations

1) sTraitChange – How do trait responses to climate change translate into demographic rates and population dynamics?

The project aims at developing a mechanistic framework that improves our ability to predict climate-induced changes across levels of organization, and generalizations of how species with different life-histories respond to climate change.

2) Pair bonds beyond the breeding season

In this project, Dr. Antica Culina uses data on multiple populations of Great tit to study causes and consequences of divorce and pair fidelity.

3) EVOCLIM – Phenotypic selection and population demography in fluctuating environments

4) Why do tits (Paridae) cover their eggs before incubation? The roles of temperature, nest predators and information parasites

Dr. Olli Loukola uses data on multiple tit populations to investigate variation in great and blue tits' egg covering behaviour across different populations in Europe and variables that may explain the geographical variation.

5) Quantifying intra-specific variation in sensitivity to climate change

This project uses sliding window analyses to study how phenological sensitivity to temperature varies among European populations of great and blue tits. The project then seeks to understand how such variation may be driven by differences in the biotic and abiotic environment experienced by each population.

6) Can we use multivariate autoregressive state-space models to quantify species interactions from time series data?

In this project Dr. Emily Simmonds and Prof. Bob O’Hara use Bayesian hierarchical models, including observation error, to try and quantify the strength of competitive interactions. This work predominantly uses simulated data to test model performance, but also uses multiple populations of great tits and blue tits as a case study illustration.

List of articles that use multiple populations of hole-nesters

• Both C., J. J. Sanz, A. A. Artemyev, B. Blaauw, R. J. Cowie, A. J. Dekhuijzen, A. Enemar, A. Järvinen, N. E. I. Nyholm, J. Potti, P.-A. Ravussin, B. Silverin, F. M. Slater, L. V. Sokolov, M.E. Visser, W. Winkel, J. Wright & H. Zang 2006. Pied flycatchers travelling from Africa to breed in Europe: differential effects of winter and migration conditions on breeding date. Ardea 94: 511-525
• Both C., A.V. Artemyev, B. Blaauw, R.J. Cowie, A.J. Dekhuizen, T. Eeva, A. Enemar, L. Gustafsson, E.V. Ivankina, A. Järvinen, N.B. Metcalfe, N.E.I. Nyholm, J. Potti, P.-A. Ravussin, J.J. Sanz, B. Silverin, F.M. Slater, L.V. Sokolov, J. Török, W. Winkel, J. Wright, H. Zang & M.E. Visser 2004. Large-scale geographical variation confirms that climate change causes birds to lay earlier. Proc. R. Soc. Lond. 271: 1657-1662.
• Burger, C., E. Belskii, T. Eeva, T. Laaksonen, M. Mägi, R. Mänd A. Qvarnström, T. Slagsvold, T. Veen, M.E. Visser, K.L. Wiebe, C. Wiley, J. Wright & C. Both 2012 Climate change, breeding date and nestling diet: how temperature differentially affects seasonal changes in pied flycatcher diet depending on habitat variation. J Anim Ecol 81: 926–936
• Dingemanse N, Bouwman KM, van de Pol M, Van Overveld T, Patrick SC, Matthysen E, Quinn J. 2012. Variation in personality and behavioural plasticity across four populations of the great tit Parus major. J Anim Ecol 81: 116-126.
• Eeva, T., S. Ruuskanen, J.-P.Salminen, E. Belskii, A. Järvinen, A. Kerimov, E. Korpimäki, I. Krams, J. Moreno, C. Morosinotto, R. Mänd, M. Orell, A. Qvarnström, H. Siitari, F.M. Slater, V. Tilgar, M.E. Visser, W. Winkel, H. Zang & T. Laaksonen 2011 Geographical trends in the yolk carotenoid composition of the pied flycatcher (Ficedula hypoleuca) Oecologia 165:277–287
• Gamelon M, Vriend SJG, Engen S, Adriaensen F, Dhondt AA, Evans SR, Matthysen E, Sheldon BC, Saether B-E. 2019. Accounting for interspecific competition and age structure in demographic analyses of density dependence improves predictions of fluctuations in population size. Ecology Letters, in press https://doi.org/10.1111/ele.13237
• Jones, W., K. Kulma, S. Bensch, M. Cichoń, A. Kerimov, M. Krist, T. Laaksonen, J. Moreno, P. Munclinger, F. Slater, E. Szöllősi, M.E. Visser & A. Qvarnström 2018 Interspecific transfer of parasites following a range-shift in Ficedula flycatchers. Ecology & Evolution 8: 12183–12192
• Korsten P, Mueller JC, Hermannstädter C, Bouwman KM, Dingemanse NJ, Drent PJ, Liedvogel M, Matthysen E, van Oers K, van Overveld T, Patrick SC, Quinn JL, Sheldon BC, Tinbergen JM, Kempenaers B. 2010. Association between DRD4 gene polymorphism and personality variation in great tits: a test across four wild populations. Molecular Ecology 19: 832-843.
• Lemoine, M., B. Doligez, K. Lucek, V. Saladin, F. Adriaensen, E. Barba, E.J. Belda, A. Charmantier, M. Cichoń, T. Eeva, A. Grégoire, C.A. Hinde, A. Johnsen, J. Komdeur, R. Mänd, E. Matthysen, A.C. Norte, N. Pitala, B.C. Sheldon, T. Slagsvold, J.M. Tinbergen, J. Török, R. Ubels, K. van Oers, M.E. Visser & H. Richner 2016 Low genetic differentiation shaped by environmental factors in a passerine bird: on the potential role of partial migration in gene flow. Biological journal of the Linnean society 118, 668–685
• Morales, J., S. Ruuskanen, T. Laaksonen, R. Mateo, E. Belskii, T. Eeva, A. Järvinen, A. Kerimov, E. Korpimäki, I. Krams, C. Morosinotto, R. Mänd, M. Orell, A. Qvarnström, H. Siitari, F.M. Slater, V. Tilgar, M.E. Visser, W. Winkel, H. Zang & J. Moreno 2013 Variation in eggshell traits between geographically distant populations of pied flycatchers Ficedula hypoleuca J Avian Biol 44: 111–120
• Mueller J, Korsten P, Hermannstaedter C, Feulner T, Dingemanse N, Matthysen E, van Oers K, van Overveld T, Patrick S, Quinn J, Riemenschneider M, Tinbergen J, Kempenaers B. 2013. Haplotype structure, adaptive history and associations with exporatory behavior of the DRD4 gene region in four great tit (Parus major) populations. Mol Ecol 22: 2797-2809
• Radchuk V, Reed T, Teplitsky, C, van de Pol M, Charmantier A, Hassall C, Adamik P, Adriaensen F, Ahola M, Arcese P, Avilés JM, Balbontin J, Blanckenhorn W, Borras A, Burthe S, Clobert J, Dehnhard N, de Lope F, Dhondt AA, Dingemanse NJ, Doi H, Eeva T, Fickel J, Filella I, Fossoy F, Goodenough AE, Hall SJG, Hansson B, Harris M, Hasselquiest D, Hickler T, Joshi J, Kharouba H, Martinez JG, Mihoub J-B, Mills JA, Molina-Morales M, Moksnes A, Ozgull A, Parejo D, Pilard P, Poisbleau M, Rousset F, Rödel M-O, Scott D, Senar JC, Stefanescu C, Stokke BG, Tamotsu K, Tarka M, Tarwater C, Thonicke K, Thorley J, Wilting A, Tryjanowski P, Merilä J, Sheldon B, Moller AP, Matthysen E, Janzen F, Dobson S, Visser ME, Beissinger SR, Courtiol A & Kramer-Schadt S. Adaptive responses of animals to climate change: not universal, likely insufficient. Nature Communications, in press.
• Ruuskanen, S., H. Siitari, T. Eeva, E. Belskii, A. Järvinen, A. Kerimov, I. Krams, J. Moreno, C. Morosinotto, R. Mänd, E. Möstl, M. Orell, A. Qvarnström, J.-P. Salminen, F. Slater, V. Tilgar, M.E. Visser, W. Winkel, H. Zang & T. Laaksonen 2011 Geographical variation in egg mass and egg content in a Passerine bird PLoS ONE 6: e25360
• Ruuskanen, S., J. Morales, T. Laaksonen, J. Moreno ,R. Mateo, E. Belskii, A. Bushuev, A. Järvinen, A. Kerimov, I. Krams, C. Morosinotto, R. Mänd, M. Orell, A. Qvarnström, F. Slater, H. Siitari V. Tilgar, M.E. Visser, W. Winkel, H. Zang & T. Eeva 2014 Large-scale geographical variation in eggshell heavy metal and calcium content in a passerine bird (Ficedula hypoleuca). Environmental Science and Pollution Research 21: 3304-3317
• Samplonius, J.M., L. Bartošová, M.D. Burgess, A.V. Bushuev, T. Eeva, E.V. Ivankina, A.B. Kerimov, I. Krams, T. Laaksonen, M. Mägi, R. Mänd, J. Potti, J. Török, M. Trnka, M.E. Visser, H. Zang & C. Both 2018 Phenological sensitivity to climate change is higher in resident than in migrant bird populations among European cavity breeders Global Change Biology 24:3780–3790
• Saether BE, Engen S, Møller AP, Visser ME, Matthysen E, Fiedler W,  Lambrechts MM, Becker P, Brommer JE, Dickinson J, du Feu C, Gehlbach FR, Merilä J, Rendell W, Thomson D, Török J. 2005. Time to extinction of bird populations. Ecology 86: 693-700.
• Saether BE, Engen S, Møller AP, Weimerskirch H, Visser ME, Fiedler W, Matthysen E, Lambrechts MM, Freckleton R, Badyaev A, Becker PH, Brommer JE, Bukacinski D, Bukacinska M, Christensen H, Dickinson J, du Feu C, Gehlbach FR, Heg D, Hötker H, Merilä J, Nielsen JT, Rendell W, Thomson D, Török J, Van Hecke P. Life history variation predicts stochastic effects on avian population dynamics. 2004. Amer. Nat. 164: 793-802.
• Sæther B-E, Engen S, Møller AP, Matthysen E, Adriaensen F, Fiedler W, Leivits A, Lambrechts MM, Visser ME, Anker-Nilssen T, Both C, Dhondt AA, McCleery RH, McMeeking J, Potti J, Røstad OW and Thomson D. 2003. Climate variation and regional gradients in population dynamics of two hole nesting passerines. Proc. R.Soc. Lond. B 270: 2397-2404.
• Sæther, B-E, S. Engen, V. Grøtan. W. Fiedler, E. Matthysen, M.E. Visser, J. Wright, A.P. Møller, F. Adriaensen, H. van Balen, D. Balmer, M.C. Mainwaring, R.H. McCleery, M. Pampus & W. Winkel 2007 The extended Moran effect and large-scale synchronous fluctuations in the size of great tit and blue tit populations J. Anim. Ecol. 76: 315-325
• Sæther B.-E., S. Engen, A. P. Møller, E. Matthysen, F. Adriaensen, W. Fiedler, A. Leivits, M. M. Lambrechts, M.E. Visser, T. Anker-Nilssen, B. C., A. Dhondt, R. H. McCleery, J. McMeeking, J. Potti, O. W. Røstad, and D. Thomson 2003 Climate variation and regional gradients in population dynamics of two hole nesting passerines. Proc. R. Soc. Lond. B 270:2397-2404
• Stenseth NC, Durant JM, Fowler MS, Matthysen E, Adriaensen F, Jonzén N, Chan K-S, Liu H, De Laet J, Sheldon BC, Visser ME, Dhondt AA. 2015. Testing for effects of climate change on competitive relationships and coexistence between two bird species. Proc Roy Soc B 282: 20141958 DOI: 10.1098/rspb.2014.1958
• Van den Steen, E., R. Pinxten, V.L.B. Jaspers, A. Covaci, E. Barba, C. Carere, M. Cichoń, A. Dubiec, T. Eeva, P. Heeb, B. Kempenaers, J.T. Lifjeld, T. Lubjuhn, R. Mänd, B. Massa, J.Å. Nilsson, A.C. Norte, M. Orell, P. Podzemny, J. J. Sanz, J.Carlos, J.J. Soler Senar, A. Sorace, J. Török, M.E. Visser, W. Winkel & M. Eens 2009 Brominated flame retardants and organochlorines in the European environment using great tit eggs as a biomonitoring tool. Environment International 35: 310-317
• Visser M.E., F. Adriaensen, J.H. van Balen, J. Blondel, A.A. Dhondt, S. van Dongen, C. du Feu, E.V. Ivankina, A.B. Kerimov, J. de Laet, E. Matthysen, R. McCleery, M. Orell & D.L. Thomson 2003. Variable responses to large-scale climate change in European Parus populations. Proc. R. Soc. Lond. B. 270: 367-372.

18.12.2019

SPI-Birds team member Stefan Vriend visited the Animal Ecology group at Radboud University in Nijmegen and talked about the value of short-term and long-term breeding data of marked individuals, the increasing need to establish a well-defined community for data archiving, standardization and access, and the objectives and workflow of SPI-Birds Network and Database. Find a link here to the slides of his presentation (NB: part of the content is made by Liam Bailey).

16.12.2019

The final Newsletter of 2019 is now out. In this newsletter we summarize what we have achieved in 2019, the year in which SPI-Birds have launched. We also look into our exciting plans for 2020, which include a new team member, Dr. Chloé Nater, SPI-Birds paper, and introduction of SPI-Birds Technical reports. And of course, the continuous increase in the number of populations with the pipelines for data standardization. 

21.10.2019 

In our third Newsletter we introduce: 1) new data and pipelines added to the database; 2) the pipeline code that transforms data into a standard format has now been published online 3) data quality checks preformed on the original data to detect any potential errors.

19.08.2019 

Our second Newsletter updates on:1) several new populations for which the pipelines have been created; 2) the newest version of the standard protocol (i.e. a standard format in which any data are mapped onto using the pipelines); 3) construction of the quality check of the data, currently underway.

Version 1.0.0 of the standard protocol for bird breeding data is available here.

20.06.2019 

We are excited to publish the first SPI-Birds Newsletter! With this first issue, we officially launch SPI-Birds, and introduce SPI-Birds team members.