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9. Connecting the data landscape of long‐term ecological studies: the SPI‐Birds data hub

Author

Culina, Antica, Adriaensen, Frank, Bailey, Liam, Burgess, Malcolm, Charmantier, Anne, Cole, Ella, Eeva, Tapio, Matthysen, Erik, Nater, Chloé, Sheldon, Ben, Sæther, Bernt‐erik, Vriend, Stefan J.G., Zajkova, Zuzana, Adamík, Peter, Aplin, Lucy, Angulo, Elena, Artemyev, Alexandr, Barba, Emilio, Barišić, Sanja, Belda, Eduardo, Can Bilgin, C., Bleu, Josefa, Both, Christiaan, Bouwhuis, Sandra, Branston, Claire, Broggi, Juli, Burke, Terry, Bushuev, Andrey, Camacho, Carlos, Campobello, Daniela, Canal, David, Cantarero, Alejandro, Caro, Samuel, Cauchoix, Maxime, Chaine, Alexis, Cichoń, Mariusz, Ćiković, Davor, Cusimano, Camillo, Deimel, Caroline, Dhondt, André, Dingemanse, Niels, Doligez, Blandine, Dominoni, Davide, Doutrelant, Claire, Drobniak, Szymon, Dubiec, Anna, Eens, Marcel, Erikstad, Kjell Einar, Espín, Silvia, Farine, Damien, Figuerola, Jordi, Kavak Gülbeyaz, Pinar, Grégoire, Arnaud, Hartley, Ian, Hau, Michaela, Hegyi, Gergely, Hille, Sabine, Hinde, Camilla, Holtmann, Benedikt, Ilyina, Tatyana, Isaksson, Caroline, Iserbyt, Arne, Ivankina, Elena, Kania, Wojciech, Kempenaers, Bart, Kerimov, Anvar, Komdeur, Jan, Korsten, Peter, Král, Miroslav, Krist, Miloš, Lambrechts, Marcel, Lara, Carlos, Leivits, Agu, Liker, András, Lodjak, Jaanis, Mägi, Marko, Mainwaring, Mark, Mänd, Raivo, Massa, Bruno, Massemin, Sylvie, Martínez‐padilla, Jesús, Mazgajski, Tomasz, Mennerat, Adele, Moreno, Juan, Mouchet, Alexia, Nakagawa, Shinichi, Nilsson, Jan‐åke, Nilsson, Johan, Norte, Ana Cláudia, Oers, Kees Van, Orell, Markku, Potti, Jaime, Quinn, John, Réale, Denis, Reiertsen, Tone Kristin, Rosivall, Balázs, Russel, Andrew, Rytkönen, Seppo, Sánchez‐virosta, Pablo, Santos, Eduardo S.A., Schroeder, Julia, Senar, Juan Carlos, Seress, Gábor, Slagsvold, Tore, Szulkin, Marta, Teplitsky, Céline, Tilgar, Vallo, Tolstoguzov, Andrey, Török, János, Valcu, Mihai, Vatka, Emma, Verhulst, Simon, Visser, Marcel, Watson, Hannah, Yuta, Teru, Zamora‐marín, José, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), University of Antwerp (UA), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, University of Exeter, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Oxford, University of Turku, Trondheim University, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
FAIR data, long-term studies, MESH: animals, meta-data standards, research network, birds, MESH: birds, [SDE]Environmental Sciences, MESH: databases, factual, MESH: metadata, data standards, database
Abstract

International audience; The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change).To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)—a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting.SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language).The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.

Published
2021

13. Connected data landscape of long-term ecological studies: the SPI-Birds data hub

Author

Adriaensen, Frank, Visser, Marcel, Branston, Claire, Drobniak, Szymon, Sánchez-Virosta, Pablo, Bailey, Liam, Figuerola, Jordi, Aplin, Lucy, Kania, Wojciech, Sæther, Bernt-Erik, Chaine, Alexis, Komdeur, Jan, Cantarero, Alejandro, Burke, Terry, Török, János, Szulkin, Marta, Gülbeyaz, Pınar, Liker, Andras, Zamora-Marín, José, Bouwhuis, Sandra, Tilgar, Vallo, Massemin, Sylvie, Mägi, Marko, Dominoni, Davide, Doligez, Blandine, Rytkönen, Seppo, Dingemanse, Niels, Nilsson, Johan, Eens, Marcel, Krist, Miloš, Norte, Ana, Bushuev, Andrey, Barišić, Sanja, Both, Christiaan, Cole, Ella, Valcu, Mihai, Reiertsen, Tone, Teplitsky, Celine, Senar, Juan, Holtmann, Benedikt, Hille, Sabine, Seress, Gábor, Santos, Eduardo, Hinde, Camilla, REALE, Denis, Hartley, Ian, Ilyina, Tatyana, Orell, Markku, Broggi, Juli, Nater, Chloé, Hau, Michaela, Grégoire, Arnaud, Rosivall, Balázs, Culina, Antica, Leivits, Agu, Lodjak, Jaanis, Erikstad, Kjell, Eeva, Tapio, Lara, Carlos, Bilgin, C., Farine, Damien, Yuta, Teru, Russel, Andrew, Mennerat, Adele, Sheldon, Benjamin, Cichoń, Mariusz, Potti, Jaime, Camacho, Carlos, Hegyi, Gergely, Cusimano, Camillo, Mainwaring, Mark, Dhondt, André, Moreno, Juan, Ćiković, Davor, Korsten, Peter, Slagsvold, Tore, Mazgajski, Tomasz, Kerimov, Anvar, Lambrechts, Marcel, Nilsson, Jan-Åke, Barba, Emilio, Espín, Silvia, Watson, Hannah, Verhulst, Simon, Caro, Samuel, Nakagawa, Shinichi, Canal, David, Belda, Eduardo, Bleu, Josefa, Mouchet, Alexia, Charmantier, Anne, Mänd, Raivo, Vatka, Emma, Doutrelant, Claire, Angulo, Elena, Quinn, John, Burgess, Malcolm, Adamík, Peter, Martínez-Padilla, Jesús, Vriend, Stefan, Iserbyt, Arne, Tolstoguzov, Andrey, Isaksson, Caroline, Král, Miroslav, van Oers, Kees, Deimel, Caroline, Artemyev, Alexandr, Dubiec, Anna, Campobello, Daniela, Kempenaers, Bart, Massa, Bruno, Matthysen, Erik, Ivankina, Elena, Cauchoix, Maxime, and Schroeder, Julia

Subjects
bepress|Life Sciences, bepress|Life Sciences|Ecology and Evolutionary Biology
Abstract

The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Further, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-terms studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org) – a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within a year of the establishment, SPI-Birds counts 120 members working on more than 80 populations, with data concerning breeding attempts of almost a million individual birds over a 1700 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration, and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by of Findable, Accessible, Interoperable, and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.

Published
2020

15. Connecting the data landscape of long‐term ecological studies: The SPI‐Birds data hub

Author

Culina, Antica, primary, Adriaensen, Frank, additional, Bailey, Liam D., additional, Burgess, Malcolm D., additional, Charmantier, Anne, additional, Cole, Ella F., additional, Eeva, Tapio, additional, Matthysen, Erik, additional, Nater, Chloé R., additional, Sheldon, Ben C., additional, Sæther, Bernt‐Erik, additional, Vriend, Stefan J. G., additional, Zajkova, Zuzana, additional, Adamík, Peter, additional, Aplin, Lucy M., additional, Angulo, Elena, additional, Artemyev, Alexandr, additional, Barba, Emilio, additional, Barišić, Sanja, additional, Belda, Eduardo, additional, Bilgin, Cemal Can, additional, Bleu, Josefa, additional, Both, Christiaan, additional, Bouwhuis, Sandra, additional, Branston, Claire J., additional, Broggi, Juli, additional, Burke, Terry, additional, Bushuev, Andrey, additional, Camacho, Carlos, additional, Campobello, Daniela, additional, Canal, David, additional, Cantarero, Alejandro, additional, Caro, Samuel P., additional, Cauchoix, Maxime, additional, Chaine, Alexis, additional, Cichoń, Mariusz, additional, Ćiković, Davor, additional, Cusimano, Camillo A., additional, Deimel, Caroline, additional, Dhondt, André A., additional, Dingemanse, Niels J., additional, Doligez, Blandine, additional, Dominoni, Davide M., additional, Doutrelant, Claire, additional, Drobniak, Szymon M., additional, Dubiec, Anna, additional, Eens, Marcel, additional, Einar Erikstad, Kjell, additional, Espín, Silvia, additional, Farine, Damien R., additional, Figuerola, Jordi, additional, Kavak Gülbeyaz, Pınar, additional, Grégoire, Arnaud, additional, Hartley, Ian R., additional, Hau, Michaela, additional, Hegyi, Gergely, additional, Hille, Sabine, additional, Hinde, Camilla A., additional, Holtmann, Benedikt, additional, Ilyina, Tatyana, additional, Isaksson, Caroline, additional, Iserbyt, Arne, additional, Ivankina, Elena, additional, Kania, Wojciech, additional, Kempenaers, Bart, additional, Kerimov, Anvar, additional, Komdeur, Jan, additional, Korsten, Peter, additional, Král, Miroslav, additional, Krist, Miloš, additional, Lambrechts, Marcel, additional, Lara, Carlos E., additional, Leivits, Agu, additional, Liker, András, additional, Lodjak, Jaanis, additional, Mägi, Marko, additional, Mainwaring, Mark C., additional, Mänd, Raivo, additional, Massa, Bruno, additional, Massemin, Sylvie, additional, Martínez‐Padilla, Jesús, additional, Mazgajski, Tomasz D., additional, Mennerat, Adèle, additional, Moreno, Juan, additional, Mouchet, Alexia, additional, Nakagawa, Shinichi, additional, Nilsson, Jan‐Åke, additional, Nilsson, Johan F., additional, Cláudia Norte, Ana, additional, van Oers, Kees, additional, Orell, Markku, additional, Potti, Jaime, additional, Quinn, John L., additional, Réale, Denis, additional, Kristin Reiertsen, Tone, additional, Rosivall, Balázs, additional, Russell, Andrew F, additional, Rytkönen, Seppo, additional, Sánchez‐Virosta, Pablo, additional, Santos, Eduardo S. A., additional, Schroeder, Julia, additional, Senar, Juan Carlos, additional, Seress, Gábor, additional, Slagsvold, Tore, additional, Szulkin, Marta, additional, Teplitsky, Céline, additional, Tilgar, Vallo, additional, Tolstoguzov, Andrey, additional, Török, János, additional, Valcu, Mihai, additional, Vatka, Emma, additional, Verhulst, Simon, additional, Watson, Hannah, additional, Yuta, Teru, additional, Zamora‐Marín, José M., additional, and Visser, Marcel E., additional

Published
2020
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16. The association between personalities, alternative breeding strategies and reproductive success in dunnocks.

Author

Holtmann, Benedikt, Lara, Carlos E., Santos, Eduardo S. A., Gillum, Joanne E., Gemmell, Neil J., and Nakagawa, Shinichi

Subjects
*BIOLOGICAL fitness, *ASSORTATIVE mating, *SEXUAL dimorphism, *SOCIAL impact, *POLYGAMY
Abstract

Although consistent between‐individual differences in behaviour (i.e. animal personality) are ubiquitous in natural populations, relatively few studies have examined how personalities influence the formation of social relationships. Yet, behavioural characteristics of both sexes might be key when it comes to pair‐bond formation, and cooperation with partners to successfully rear offspring. We here use a wild population of dunnocks (Prunella modularis) to first investigate whether individuals mate nonrandomly (i.e. assortative mating) with regard to four behavioural traits—flight‐initiation distance (FID), provisioning, activity and vigilance—that differ in repeatability and have previously been associated with mating patterns and fitness in other species. Second, we test whether an individual's FID is associated with variability in the dunnocks' mating system (i.e. monogamous pairs vs. polygamous groups). Finally, we determine whether FID and provisioning of males and females associate with their reproductive success. We found no statistical support for assortative mating in FID between males and females. Interestingly, in polygamous groups, co‐breeding males differed in their FIDs with dominant alpha males having significantly shorter FIDs compared with subordinate beta‐males. Moreover, there was evidence for assortative mating in provisioning for alpha males and females in polygamous groups. We also found that male provisioning influenced reproductive success of both sexes, whereas female provisioning rates only positively correlated with her own but not their partner(s) reproductive output. Our results suggest that personality differences may have important implications for social relationships, the emergence of different mating patterns and ultimately reproductive success within populations. [ABSTRACT FROM AUTHOR]

Published
2022
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17. Strong phenotypic trait correlations between mating partners do not result from assortative mating in wild great tits (Parus major).

Author

Holtmann, Benedikt and Dingemanse, Niels J.

Subjects
*ASSORTATIVE mating, *GREAT tit, *PHENOTYPES, *MEASUREMENT errors, *PHENOTYPIC plasticity
Abstract

There is considerable debate about the occurrence of assortative mating between phenotypic traits measured within natural populations. Meta‐analyses have implied that assortative mating occurs generally in natural populations, but recent work indicates these conclusions largely result from biased data. Specifically, estimates of phenotypic correlations between mating partners do not solely result from nonrandom associations between individual‐level traits of partners but also from other biological processes (joint phenotypic plasticity, indirect genetic effects), methodological practices (observer bias) and other unexplained residual correlations (e.g. correlated measurement error). This paper puts this critique to test. First, we estimated the overall phenotypic correlation between phenotypic traits of mating partners for a wild population of great tits. Second, we estimated various key variance components to reveal the extent to which phenotypic correlations between partners resulted from assortative mating, reversible plasticity, social partner effects and methodological practices. We performed our analyses for a range of phenotypic traits (body mass, breathing rate, exploration behaviour, wing and tarsus length) to derive general conclusions not hinging on the specifics of the traits involved. Our analyses support the conclusion that patterns of assortative mating exist at first glance but occur because of the biasing effects of correlated residuals likely caused by a combination of phenotypic responses to unknown environmental factors or measurement error—not because of intrinsic patterns of assortative mating. [ABSTRACT FROM AUTHOR]

Published
2022
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21. Parental feeding decisions in dunnocks from a resource availability perspective: assessing the role of nestling tongue spots and body size

Author

Holtmann, Benedikt, Lara, Carlos, Santos , Eduardo, and Nakagawa , Shinichi

Subjects
bepress|Life Sciences, bepress|Life Sciences|Ecology and Evolutionary Biology|Behavior and Ethology, bepress|Life Sciences|Ecology and Evolutionary Biology, bepress|Life Sciences|Ecology and Evolutionary Biology|Evolution
Abstract

A recent comparative study found that when resources are limited, parents primarily allocate food to superior nestlings, whereas when resources are abundant, parents evenly allocate food to all nestlings, putting forward what we refer to as the resource availability hypothesis (RAH). This ecological perspective adds valuable insights to the two classical hypotheses, sexual conflict and parent–offspring conflict, that explain the diversity of feeding patterns observed in nature. We investigated the parental allocation decisions between monogamous pairs and polyandrous trios of dunnocks. We first assessed whether the number of spots on the tongues of nestlings signals condition to the breeding parents. We then explored the RAH in an intra-specific context. We found evidence to suggest that the number of nestling tongue spots signals condition to breeding parents. We also found that monogamous and polyandrous females and polyandrous males prioritized nestlings in better condition, yet monogamous males fed nestlings evenly. This finding is consistent with the RAH in our population if monogamous males secure more resources due to their superior quality, thus resulting in the even feeding of nestlings. Another explanation for the observed parental feeding decisions that is indirectly associated with the RAH is sexual conflict (the uncertainty of paternity). Finally, we found that an assumption regarding feeding patterns in dunnocks that was established in another population was not fulfilled here; thus, it is worth noting that testing assumptions is a vital step towards assessing the generality of former findings, paving the way to credible scientific practice.

Published
2018

25. Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub.

Author

Culina A, Adriaensen F, Bailey LD, Burgess MD, Charmantier A, Cole EF, Eeva T, Matthysen E, Nater CR, Sheldon BC, Saether BE, Vriend SJG, Zajkova Z, Adamík P, Aplin LM, Angulo E, Artemyev A, Barba E, Barišić S, Belda E, Bilgin CC, Bleu J, Both C, Bouwhuis S, Branston CJ, Broggi J, Burke T, Bushuev A, Camacho C, Campobello D, Canal D, Cantarero A, Caro SP, Cauchoix M, Chaine A, Cichoń M, Ćiković D, Cusimano CA, Deimel C, Dhondt AA, Dingemanse NJ, Doligez B, Dominoni DM, Doutrelant C, Drobniak SM, Dubiec A, Eens M, Einar Erikstad K, Espín S, Farine DR, Figuerola J, Kavak Gülbeyaz P, Grégoire A, Hartley IR, Hau M, Hegyi G, Hille S, Hinde CA, Holtmann B, Ilyina T, Isaksson C, Iserbyt A, Ivankina E, Kania W, Kempenaers B, Kerimov A, Komdeur J, Korsten P, Král M, Krist M, Lambrechts M, Lara CE, Leivits A, Liker A, Lodjak J, Mägi M, Mainwaring MC, Mänd R, Massa B, Massemin S, Martínez-Padilla J, Mazgajski TD, Mennerat A, Moreno J, Mouchet A, Nakagawa S, Nilsson JÅ, Nilsson JF, Cláudia Norte A, van Oers K, Orell M, Potti J, Quinn JL, Réale D, Kristin Reiertsen T, Rosivall B, Russell AF, Rytkönen S, Sánchez-Virosta P, Santos ESA, Schroeder J, Senar JC, Seress G, Slagsvold T, Szulkin M, Teplitsky C, Tilgar V, Tolstoguzov A, Török J, Valcu M, Vatka E, Verhulst S, Watson H, Yuta T, Zamora-Marín JM, and Visser ME

Subjects
Animals, Databases, Factual, Birds, Metadata
Abstract

The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration., (© 2020 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Published
2021
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