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3. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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4. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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6. Multi-decadal improvements in the ecological quality of European rivers are not consistently reflected in biodiversity metrics

Author

Sinclair, James S., Welti, Ellen A. R., Altermatt, Florian, Álvarez-Cabria, Mario, Aroviita, Jukka, Baker, Nathan J., Barešová, Libuše, Barquín, José, Bonacina, Luca, Bonada, Núria, Cañedo-Argüelles, Miguel, Csabai, Zoltán, de Eyto, Elvira, Dohet, Alain, Dörflinger, Gerald, Eriksen, Tor E., Evtimova, Vesela, Feio, Maria J., Ferréol, Martial, Floury, Mathieu, Forio, Marie Anne Eurie, Fornaroli, Riccardo, Goethals, Peter L. M., Heino, Jani, Hering, Daniel, Huttunen, Kaisa-Leena, Jähnig, Sonja C., Johnson, Richard K., Kuglerová, Lenka, Kupilas, Benjamin, L’Hoste, Lionel, Larrañaga, Aitor, Leitner, Patrick, Lorenz, Armin W., McKie, Brendan G., Muotka, Timo, Osadčaja, Diana, Paavola, Riku, Palinauskas, Vaidas, Pařil, Petr, Pilotto, Francesca, Polášek, Marek, Rasmussen, Jes J., Schäfer, Ralf B., Schmidt-Kloiber, Astrid, Scotti, Alberto, Skuja, Agnija, Straka, Michal, Stubbington, Rachel, Timm, Henn, Tyufekchieva, Violeta, Tziortzis, Iakovos, Vannevel, Rudy, Várbíró, Gábor, Velle, Gaute, Verdonschot, Ralf C. M., Vray, Sarah, and Haase, Peter

Published
2024
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13. Multi-decadal improvements in the ecological quality of European rivers are not consistently reflected in biodiversity metrics

Author

0000-0003-0787-7342, 0000-0001-6944-3422, 0000-0002-4831-6958, 0000-0001-7948-106X, 0000-0003-1897-2636, 0000-0002-4695-5932, 0000-0002-2983-3335, 0000-0003-3864-7451, 0000-0003-1700-2574, 0000-0003-2281-2491, 0000-0003-2962-7387, 0000-0003-0209-4648, 0000-0003-2033-6399, 0000-0002-6358-8011, 0000-0003-0362-6802, 0000-0001-6740-3654, 0000-0002-4952-5807, 0000-0001-6675-4751, 0000-0001-6326-5653, 0000-0003-0488-1274, 0000-0002-6349-9561, 0000-0001-7979-6563, 0000-0003-0239-9468, 0000-0002-0185-9154, 0000-0002-3262-6396, 0009-0006-6199-9200, 0000-0002-4708-1413, 0000-0002-4714-0305, 0000-0002-7471-997X, 0000-0003-1848-3154, 0000-0002-5932-3125, 0000-0001-8839-5913, 0000-0002-5861-7551, 0000-0001-8475-5109, 0000-0002-9315-7773, 0000-0002-5603-271X, 0000-0002-0977-5975, 0000-0002-7385-8302, 0000-0002-9340-0438, Sinclair, James S., Welti, Ellen A. R., Altermatt, Florian, Álvarez-Cabria, Mario, Aroviita, Jukka, Baker, Nathan J., Barešová, Libuše, Barquín, José, Bonacina, Luca, Bonada, Núria, Cañedo-Argüelles, Miguel, Csabai, Zoltán, de Eyto, Elvira, Dohet, Alain, Dörflinger, Gerald, Eriksen, Tor E., Evtimova, Vesela, Feio, Maria J., Ferréol, Martial, Floury, Mathieu, Forio, Marie Anne Eurie, Fornaroli, Riccardo, Goethals, Peter L. M., Heino, Jani, Hering, Daniel, Huttunen, Kaisa-Leena, Jähnig, Sonja C., Johnson, Richard K., Kuglerová, Lenka, Kupilas, Benjamin, L'Hoste, Lionel, Larrañaga, Aitor, Leitner, Patrick, Lorenz, Armin W., McKie, Brendan G., Muotka, Timo, Osadčaja, Diana, Paavola, Riku, Palinauskas, Vaidas, Pařil, Petr, Pilotto, Francesca, Polášek, Marek, Rasmussen, Jes J., Schäfer, Ralf B., Schmidt-Kloiber, Astrid, Scotti, Alberto, Skuja, Agnija, Straka, Michal, Stubbington, Rachel, Timm, Henn, Tyufekchieva, Violeta, Tziortzis, Iakovos, Vannevel, Rudy, Várbíró, Gábor, Velle, Gaute, Verdonschot, Ralf C. M., Vray, Sarah, Haase, Peter, 0000-0003-0787-7342, 0000-0001-6944-3422, 0000-0002-4831-6958, 0000-0001-7948-106X, 0000-0003-1897-2636, 0000-0002-4695-5932, 0000-0002-2983-3335, 0000-0003-3864-7451, 0000-0003-1700-2574, 0000-0003-2281-2491, 0000-0003-2962-7387, 0000-0003-0209-4648, 0000-0003-2033-6399, 0000-0002-6358-8011, 0000-0003-0362-6802, 0000-0001-6740-3654, 0000-0002-4952-5807, 0000-0001-6675-4751, 0000-0001-6326-5653, 0000-0003-0488-1274, 0000-0002-6349-9561, 0000-0001-7979-6563, 0000-0003-0239-9468, 0000-0002-0185-9154, 0000-0002-3262-6396, 0009-0006-6199-9200, 0000-0002-4708-1413, 0000-0002-4714-0305, 0000-0002-7471-997X, 0000-0003-1848-3154, 0000-0002-5932-3125, 0000-0001-8839-5913, 0000-0002-5861-7551, 0000-0001-8475-5109, 0000-0002-9315-7773, 0000-0002-5603-271X, 0000-0002-0977-5975, 0000-0002-7385-8302, 0000-0002-9340-0438, Sinclair, James S., Welti, Ellen A. R., Altermatt, Florian, Álvarez-Cabria, Mario, Aroviita, Jukka, Baker, Nathan J., Barešová, Libuše, Barquín, José, Bonacina, Luca, Bonada, Núria, Cañedo-Argüelles, Miguel, Csabai, Zoltán, de Eyto, Elvira, Dohet, Alain, Dörflinger, Gerald, Eriksen, Tor E., Evtimova, Vesela, Feio, Maria J., Ferréol, Martial, Floury, Mathieu, Forio, Marie Anne Eurie, Fornaroli, Riccardo, Goethals, Peter L. M., Heino, Jani, Hering, Daniel, Huttunen, Kaisa-Leena, Jähnig, Sonja C., Johnson, Richard K., Kuglerová, Lenka, Kupilas, Benjamin, L'Hoste, Lionel, Larrañaga, Aitor, Leitner, Patrick, Lorenz, Armin W., McKie, Brendan G., Muotka, Timo, Osadčaja, Diana, Paavola, Riku, Palinauskas, Vaidas, Pařil, Petr, Pilotto, Francesca, Polášek, Marek, Rasmussen, Jes J., Schäfer, Ralf B., Schmidt-Kloiber, Astrid, Scotti, Alberto, Skuja, Agnija, Straka, Michal, Stubbington, Rachel, Timm, Henn, Tyufekchieva, Violeta, Tziortzis, Iakovos, Vannevel, Rudy, Várbíró, Gábor, Velle, Gaute, Verdonschot, Ralf C. M., Vray, Sarah, and Haase, Peter

Abstract

Humans impact terrestrial, marine and freshwater ecosystems, yet many broad-scale studies have found no systematic, negative biodiversity changes (for example, decreasing abundance or taxon richness). Here we show that mixed biodiversity responses may arise because community metrics show variable responses to anthropogenic impacts across broad spatial scales. We first quantified temporal trends in anthropogenic impacts for 1,365 riverine invertebrate communities from 23 European countries, based on similarity to least-impacted reference communities. Reference comparisons provide necessary, but often missing, baselines for evaluating whether communities are negatively impacted or have improved (less or more similar, respectively). We then determined whether changing impacts were consistently reflected in metrics of community abundance, taxon richness, evenness and composition. Invertebrate communities improved, that is, became more similar to reference conditions, from 1992 until the 2010s, after which improvements plateaued. Improvements were generally reflected by higher taxon richness, providing evidence that certain community metrics can broadly indicate anthropogenic impacts. However, richness responses were highly variable among sites, and we found no consistent responses in community abundance, evenness or composition. These findings suggest that, without sufficient data and careful metric selection, many common community metrics cannot reliably reflect anthropogenic impacts, helping explain the prevalence of mixed biodiversity trends.

Published
2024

16. Impact of Plasmodium relictum Infection on the Colonization Resistance of Bird Gut Microbiota: A Preliminary Study

Author

Aželytė, Justė, primary, Maitre, Apolline, additional, Abuin-Denis, Lianet, additional, Piloto-Sardiñas, Elianne, additional, Wu-Chuang, Alejandra, additional, Žiegytė, Rita, additional, Mateos-Hernández, Lourdes, additional, Obregón, Dasiel, additional, Cabezas-Cruz, Alejandro, additional, and Palinauskas, Vaidas, additional

Published
2024
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19. Raising the bar: genus-specific nested PCR improves detection and lineage identification of avian haemosporidian parasites.

Author

Musa, Sandrine, Hemberle, Theo, Bensch, Staffan, Palinauskas, Vaidas, Baltrunaite, Laima, Woog, Friederike, and Mackenstedt, Ute

Subjects
MIXED infections, CYTOCHROME b, PARASITES, PLASMODIUM, MEDICAL screening, BLOOD sampling, URBAN hospitals
Abstract

Avian haemosporidian parasites are useful model organisms to study the ecology and evolution of parasite-host interactions due to their global distribution and extensive biodiversity. Detection of these parasites has evolved from microscopic examination to PCR-based methods, with the mitochondrial cytochrome b gene serving as barcoding region. However, standard PCR protocols used for screening and identification purposes have limitations in detecting mixed infections and generating phylogenetically informative data due to short amplicon lengths. To address these issues, we developed a novel genusspecific nested PCR protocol targeting avian haemosporidian parasites. The protocol underwent rigorous testing utilizing a large dataset comprising blood samples from Malagasy birds of three distinct Passeriformes families. Furthermore, validation was done by examining smaller datasets in two other laboratories employing divergent master mixes and different bird species. Comparative analyses were conducted between the outcomes of the novel PCR protocol and those obtained through the widely used standard nested PCR method. The novel protocol enables specific identification of Plasmodium, Haemoproteus (Parahaemoproteus), and Leucocytozoon parasites. The analyses demonstrated comparable sensitivity to the standard nested PCR with notable improvements in detecting mixed infections. In addition, phylogenetic resolution is improved by amplification of longer fragments, leading to a better understanding of the haemosporidian biodiversity and evolution. Overall, the novel protocol represents a valuable addition to avian haemosporidian detection methodologies, facilitating comprehensive studies on parasite ecology, epidemiology, and evolution. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Environmental, geographical and time‐related impacts on avian malaria infections in native and introduced populations of house sparrows ( Passer domesticus ), a globally invasive species

Author

Ferraguti, Martina, Magallanes, Sergio, Jiménez‐Peñuela, Jéssica, Martínez‐de la Puente, Josué, Garcia‐Longoria, Luz, Figuerola, Jordi, Muriel, Jaime, Albayrak, Tamer, Bensch, Staffan, Bonneaud, Camille, Clarke, Rohan H., Czirják, Gábor Á., Dimitrov, Dimitar, Espinoza, Kathya, Ewen, John G., Ishtiaq, Farah, Flores‐Saavedra, Wendy, Garamszegi, László Zsolt, Hellgren, Olof, Horakova, Dita, Huyvaert, Kathryn P., Jensen, Henrik, Križanauskienė, Asta, Lima, Marcos R., Lujan‐Vega, Charlene, Magnussen, Eyðfinn, Martin, Lynn B., Matson, Kevin D., Møller, Anders Pape, Munclinger, Pavel, Palinauskas, Vaidas, Pap, Péter L., Pérez‐Tris, Javier, Renner, Swen C., Ricklefs, Robert, Scebba, Sergio, Sehgal, Ravinder N. M., Soler, Manuel, Szöllősi, Eszter, Valkiūnas, Gediminas, Westerdahl, Helena, Zehtindjiev, Pavel, and Marzal, Alfonso

Subjects
Enfermedades transmitidas por vectores, Plasmodium, Global and Planetary Change, Ecology, Parásitos hemosporidios, haemosporidian parasites, mosquito-borne pathogens, urbanization index, vector-borne diseases, purl.org/pe-repo/ocde/ford#1.05.08 [https], Patógenos transmitidos por mosquitos, Plasmodio, Wildlife Ecology and Conservation, Índice de urbanización, Ecology, Evolution, Behavior and Systematics
Abstract

AC K N OW L E D G M E N T S This study was funded by projects: IB20089 from the Consejería de Economía, Ciencia y Agenda Digital of the Junta de Extremadura and Fondo Europeo de Desarrollo Regional, P11-RNM-7038 from Junta de Andalucía, and PR(19_ECO_0070) from Ayudas Fundación BBVA a Equipos de Investigación Científica 2019. MF was supported by a Juan de la Cierva 2017 Formación contract (FJCI-2017-34394) from the Ministry of Science, Innovation and Universities, by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie (grant agreement No 844285, ‘EpiEcoMod’) and she is currently funded by a Ramón y Cajal postdoctoral contract (RYC2021- 031613-I) from the Spanish Ministry of Science and Innovation (MICINN). JJP was supported by the Fundación Tatiana Pérez de Guzmán el Bueno. JMP was supported by ProyExcel_00049 financed by Proyectos I+D+i of Junta de Andalucía 2021. LGL was supported by Junta de Extremadura (IB20089, Post-Doc grant). JM was supported by a Juan de la Cierva - Formación contract (FJCI-2017-34109) from the Ministry of Science, Innovation and Universities, and he is currently supported by a postdoctoral researcher contract for scientific excellence under the Plan Propio de I+D+i of the Universidad de Castilla - La Mancha (UCLM), co-funded by the European Social Fund Plus (ESF+). LZG was supported by funds from the Hungary's National Research, Development and Innovation Office (K135841, RRF-2.3.1-21-2022- 00006). We also acknowledge the comments of four anonymous reviewers who improved the final version of this manuscript., DATA AVA I L A B I L I T Y S TAT E M E N T Data supporting the conclusions of this study are available in the supplementary material to this article. Any further details are available from the corresponding author on reasonable request., Aim The increasing spread of vector-borne diseases has resulted in severe health concerns for humans, domestic animals and wildlife, with changes in land use and the introduction of invasive species being among the main possible causes for this increase. We explored several ecological drivers potentially affecting the local prevalence and richness of avian malaria parasite lineages in native and introduced house sparrows (Passer domesticus) populations. Location Global. Time period 2002–2019. Major taxa studied Avian Plasmodium parasites in house sparrows. Methods We analysed data from 2,220 samples from 69 localities across all continents, except Antarctica. The influence of environment (urbanization index and human density), geography (altitude, latitude, hemisphere) and time (bird breeding season and years since introduction) were analysed using generalized additive mixed models (GAMMs) and random forests. Results Overall, 670 sparrows (30.2%) were infected with 22 Plasmodium lineages. In native populations, parasite prevalence was positively related to urbanization index, with the highest prevalence values in areas with intermediate urbanization levels. Likewise, in introduced populations, prevalence was positively associated with urbanization index; however, higher infection occurred in areas with either extreme high or low levels of urbanization. In introduced populations, the number of parasite lineages increased with altitude and with the years elapsed since the establishment of sparrows in a new locality. Here, after a decline in the number of parasite lineages in the first 30 years, an increase from 40 years onwards was detected. Main conclusions Urbanization was related to parasite prevalence in both native and introduced bird populations. In invaded areas, altitude and time since bird introduction were related to the number of Plasmodium lineages found to be infecting sparrows., Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía, Grant/Award Number: P11-RNM-7038, Fundación BBVA, Grant/Award Number: PR(19_ECO_0070, Junta de Extremadura, Grant/Award Number: IB20089 and PO17024, Marie Sklodowska- Curie Actions, Grant/Award Number: 844285, Ministerio de Ciencia, Innovación y Universidades, Grant/Award Number: FJCI-2017-34109 and FJCI-2017-34394, Proyectos I+D+i of Junta de Andalucía 2021, Grant/Award Number: ProyExcel_00049, Universidad de Castilla- La Mancha

Published
2023
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24. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M, primary, Formenti, Giulio, additional, Mouton, Alice, additional, Ciofi, Claudio, additional, Waterhouse, Robert M, additional, Mazzoni, Camila J, additional, De Panis, Diego, additional, Schlude Marins, Luisa S, additional, Leitao, Henrique G, additional, Diedericks, Genevieve, additional, Kirangwa, Joseph, additional, Morselli, Marco, additional, Salces, Judit, additional, Escudero, Nuria, additional, Iannucci, Alessio, additional, Natali, Chiara, additional, Svardal, Hannes, additional, Fernandez, Rosa, additional, De Pooter, Tim, additional, Joris, Geert, additional, Strazisar, Mojca, additional, Wood, Jo, additional, Herron, Katie E, additional, Seehausen, Ole, additional, Watts, Phillip C, additional, Shaw, Felix, additional, Davey, Robert P, additional, Minotto, Alice, additional, Fernandez Gonzalez, Jose Maria, additional, Bohne, Astrid, additional, Alegria, Carla, additional, Alioto, Tyler, additional, Alves, Paulo C, additional, Amorim, Isabel R, additional, Aury, Jean-Marc, additional, Backstrom, Niclas, additional, Baldrian, Petr, additional, Ballarin, Loriano, additional, Baltrunaite, Laima, additional, Barta, Endre, additional, BedHom, Bertrand, additional, Belser, Caroline, additional, Bergsten, Johannes, additional, Bertrand, Laurie, additional, Bilandija, Helena, additional, Binzer-Panchal, Mahesh, additional, Bista, Iliana, additional, Blaxter, Mark, additional, Borges, Paulo AV, additional, Borges Dias, Guilherme, additional, Bosse, Mirte, additional, Brown, Tom, additional, Bruggmann, Remy, additional, Buena-Atienza, Elena, additional, Burgin, Josephine, additional, Buzan, Elena, additional, Casadei, Nicolas, additional, Chiara, Matteo, additional, Chozas, Sergio, additional, Ciampor, Fedor F, additional, Crottini, Angelica, additional, Cruaud, Corinne, additional, Cruz, Fernando, additional, Dalen, Love, additional, De Biase, Alessio, additional, del Campo, Javier, additional, Delic, Teo, additional, Dennis, Alice B, 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Winkler, Sylke, additional

Published
2023
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42. Additional file 1 of Genomic sequence capture of Plasmodium relictum in experimentally infected birds

Author

Ellis, Vincenzo A., Kalbskopf, Victor, Ciloglu, Arif, Duc, Mélanie, Huang, Xi, Inci, Abdullah, Bensch, Staffan, Hellgren, Olof, and Palinauskas, Vaidas

Abstract

Additional file 1: Figure S1. Sequencing coverage across the P. relictum genome. Each graph of the following figure represents the coverage of each non-archived chromosomes (i.e., chromosomes 1–14 and the apicoplast and mitochondrial genomes) from the P. relictum genome (chromosome name appears in upper left-hand side of each graph). Each panel within each of the graphs represents one sample with the sample name above the panel (names follow Additional file 5: Table S2). The y-axes were capped at 1000 sequenced bp (depth of coverage) to represent the low coverage regions at a more appropriate scale. However, the spikes often extended past 1000 bp. The x-axes are measured in kilobase pairs.

Published
2022
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43. Additional file 2 of Genomic sequence capture of Plasmodium relictum in experimentally infected birds

Author

Ellis, Vincenzo A., Kalbskopf, Victor, Ciloglu, Arif, Duc, Mélanie, Huang, Xi, Inci, Abdullah, Bensch, Staffan, Hellgren, Olof, and Palinauskas, Vaidas

Abstract

Additional file 2: Figure S2. Rarefaction curves of number of probed regions intersected by a read by at least 10 bp as a function of number of reads that mapped to any probed region (assigned reads). A rarefaction curve plotted for each sample showing the number of probed regions intersected by a read from the sample by at least 10 bp in relation to the number of reads that mapped to any probed region (assigned reads) for each sample (the “assigned reads” variable counts the same read more than once if it mapped to more than one probed region). Many of the samples reached asymptotes with relatively high number of probed regions sequenced suggesting more sequencing will not lead to large gains in coverage but may contribute to depth of coverage. Three samples of the parasite lineage SGS1 with parasitemia lower than 1% (1455, 1457, and 1458) group separately from the other SGS1 samples and the rarefaction curves suggest that they had lower numbers of probed regions intersected by a read than the other samples at similar levels of sequencing. This suggests that low parasitemia limited sequence capture success and that this limit likely cannot be fully overcome with greater sequencing. Moreover, sample 51242 (lineage GRW4) had the most sequencing of all the samples (> 15 million total reads; Additional file 5: Table S2), but still had a relatively low number of probed regions intersected by a read and relatively few assigned reads. Sample 51242 also had low parasitemia (< 1%) and represented the most divergent of the lineages (GRW4).

Published
2022
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