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3. Effect of Myxoma Virus Species Jump on Iberian Hare Populations

Author

Cardoso, Beatriz, Garcia-Bocanegra, Ignacio, Queiros, Joao, Fernandez-Lopez, Javier, Alves, Paulo C., and Acevedo, Pelayo

Subjects
Medical research, Medicine, Experimental, Myxoma virus -- Distribution, Animal populations -- Evaluation, Company distribution practices, Health
Abstract

In July 2018, after 60 years of endemic circulation in European wild rabbits (Oryctolagus cuniculus), myxoma virus (MYXV) jumped to the Iberian hare (Lepus granatensis) (1). This species jump resulted [...]

Published
2024
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5. 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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6. Building a Portuguese coalition for biodiversity genomics

Author

Marques, João P., Alves, Paulo C., Amorim, Isabel R., Lopes, Ricardo J., Moura, Monica, Myers, Eugene, Sim-sim, Manuela, Sousa-Santos, Carla, Alves, M. Judite, Borges, Paulo A. V., Brown, Thomas, Carneiro, Miguel, Carrapato, Carlos, Ceríaco, Luís M. P., Ciofi, Claúdio, da Silva, Luís P., Diedericks, Genevieve, Diroma, Maria Angela, Farelo, Liliana, Formenti, Giulio, Gil, Fátima, Grilo, Miguel, Iannucci, Alessio, Leitão, Henrique G., Máguas, Cristina, Mc Cartney, Ann M., Mendes, Sofia L., Moreno, João M., Morselli, Marco, Mouton, Alice, Natali, Chiara, Pereira, Fernando, Rego, Rúben M. C., Resendes, Roberto, Roxo, Guilherme, Svardal, Hannes, Trindade, Helena, Vicente, Sara, Winkler, Sylke, Alvarenga, Marcela, Amaral, Andreia J., Antunes, Agostinho, Campos, Paula F., Canário, Adelino V. M., Castilho, Rita, Castro, L. Filipe C., Crottini, Angelica, Cunha, Mónica V., Espregueira Themudo, Gonçalo, Esteves, Pedro J., Faria, Rui, Rodríguez Fernandes, Carlos, Ledoux, Jean-Baptiste, Louro, Bruno, Magalhaes, Sara, Paulo, Octávio S., Pearson, Gareth, Pimenta, João, Pina-Martins, Francisco, Santos, Teresa L., Serrão, Ester, Melo-Ferreira, José, and Sousa, Vítor C.

Published
2024
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7. 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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8. Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Author

Pearman, Peter B., Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo C., Aravanopoulos, F. A., Bertola, Laura D., Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela P., Fussi, Barbara, Godoy, José A., Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig R., Raeymaekers, Joost A. M., Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo N., Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank E., Guisan, Antoine, and Bruford, Michael

Published
2024
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9. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

Author

Nilson, Sara M, Gandolfi, Barbara, Grahn, Robert A, Kurushima, Jennifer D, Lipinski, Monika J, Randi, Ettore, Waly, Nashwa E, Driscoll, Carlos, Murua Escobar, Hugo, Schuster, Rolf K, Maruyama, Soichi, Labarthe, Norma, Chomel, Bruno B, Ghosh, Sankar Kumar, Ozpinar, Haydar, Rah, Hyung-Chul, Millán, Javier, Mendes-de-Almeida, Flavya, Levy, Julie K, Heitz, Elke, Scherk, Margie A, Alves, Paulo C, Decker, Jared E, and Lyons, Leslie A

Subjects
Biological Sciences, Genetics, Animals, Cats, Domestication, Genotype, Microsatellite Repeats, Middle East, Evolutionary Biology, Evolutionary biology
Abstract

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.

Published
2022

15. Mountain Hare Lepus timidus Linnaeus, 1758

Author

Angerbjörn, Anders, Schai-Braun, Stéphanie Claire, Hackländer, Klaus, Section editor, Alves, Paulo C., Section editor, Hackländer, Klaus, Series Editor, Zachos, Frank E., Series Editor, and Alves, Paulo C., editor

Published
2023
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16. Cape Hare Lepus capensis Linnaeus, 1758

Author

Scandura, Massimo, De Marinis, Anna Maria, Canu, Antonio, Hackländer, Klaus, Section editor, Alves, Paulo C., Section editor, Hackländer, Klaus, Series Editor, Zachos, Frank E., Series Editor, and Alves, Paulo C., editor

Published
2023
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18. European Rabbit Oryctolagus cuniculus (Linnaeus, 1758)

Author

Delibes-Mateos, Miguel, Rödel, Heiko G., Rouco, Carlos, Alves, Paulo C., Carneiro, Miguel, Villafuerte, Rafael, Hackländer, Klaus, Section editor, Hackländer, Klaus, Series Editor, Zachos, Frank E., Series Editor, and Alves, Paulo C., editor

Published
2023
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21. Mining the 99 Lives Cat Genome Sequencing Consortium database implicates genes and variants for the Ticked locus in domestic cats (Felis catus)

Author

Lyons, LA, Buckley, RM, Harvey, RJ, Abitbol, Marie, Aberdein, Danielle, Alves, Paulo C, Andersson, Asa Ohlsson, Bellone, Rebecca R, Bergström, Tomas F, Bilgen, Nuket, Boyko, Adam R, Brockman, Jeffrey A, Casal, Margret L, Castelhano, Marta G, Davis, Brian W, Davison, Lucy, Distl, Ottmar, Dodman, Nicholas H, Ellinwood, N Matthew, Fogle, Jonathan E, Forman, Oliver P, Garrick, Dorian J, Ginns, Edward I, Häggström, Jens, Hasegawa, Daisuke, Haase, Bianca, Jagannathan, Vidhya, Lait, Philippa, Hernandez, Isabel, Hytönen, Marjo K, Kaukonen, Maria, Kosho, Tomoki, Leclerc, Emilie, Lear, Teri L, Leeb, Tosso, Li, Ronald HL, Lohi, Hannes, Longeri, Maria, Magnuson, Mark A, Malik, Richard, Mane, Shrinivasrao P, Middleton, Rondo, Munday, John S, Murphy, William J, Myers, Alexandra N, Pedersen, Niels C, Peterson‐Jones, Simon M, Rothschild, Max F, Rusbridge, Clare, Schoenebeck, Jeffrey J, Shapiro, Beth, Stern, Joshua A, Swanson, William F, Terio, Karen A, Todhunter, Rory J, Warren, Wesley C, Wilcox, Elizabeth A, Wildschutte, Julia H, and Yu, Yoshihiko

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Amino Acid Sequence, Animals, Breeding, Cats, Genome, Hair Color, Intercellular Signaling Peptides and Proteins, Phenotype, Abyssinian, coat pattern, Dickkopf&#160, Wnt&#160, Signaling&#160, Pathway Inhibitor 4, DKK4, Tabby, Lives Cat Genome Consortium, DKK4, Dickkopf Wnt Signaling Pathway Inhibitor 4, Tabby, Zoology, Veterinary Sciences, Dairy & Animal Science
Abstract

Tabby patterns of fur coats are defining characteristics in wild and domestic felids. Historically, three autosomal alleles at one locus (Tabby): Abyssinian (Ta ; a.k.a. ticked), mackerel (Tm ; a.k.a. striped) and blotched (tb ; a.k.a. classic, blotched) were thought to control these patterns in domestic cats and their breeds. Currently, at least three loci influence cat tabby markings, two of which are designated Tabby and Ticked. The Tabby locus is laeverin (LVRN) and affects the mackerel and blotched patterns. The unidentified gene for the Ticked locus on cat chromosome B1 was suggested to control the presence or absence of the ticked pattern (Tabby - Abyssinian (Ta ; a.k.a. ticked). The cat reference genome (Cinnamon, the Abyssinian) has the ticked phenotype and the variant dataset and coat phenotypes from the 99 Lives Cat Genome Consortium (195 cats) were used to identify candidate genes and variants associated with the Ticked locus. Two strategies were used to find the Ticked allele(s), one considered Cinnamon with the reference allele or heterozygous (Strategy A) and the other considered Cinnamon as having the variant allele or heterozygous (Strategy B). For Strategy A, two variants in Dickkopf Wnt Signaling Pathway Inhibitor 4 (DKK4), a p.Cys63Tyr (B1:41621481, c.188G>A) and a less common p.Ala18Val (B1:42620835, c.53C>T) variant are suggested as two alleles influencing the Ticked phenotype. Bioinformatic and molecular modeling analysis suggests that these changes disrupt a key disulfide bond in the Dkk4 cysteine-rich domain 1 or Dkk4 signal peptide cleavage respectively. All coding variants were excluded as Ticked alleles using Strategy B.

Published
2021

28. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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29. Using GPS and accelerometer data to remotely detect breeding events in two elusive ground-nesting steppe birds.

Author

Ferraz, Gonçalo, Pacheco, Carlos, Fernández-Tizón, Mario, Marques, Ana T., Alves, Paulo C., Silva, João P., and Mougeot, François

Abstract

Background: Modern biologging technologies allow researchers to gain a better understanding of animal movements, offering opportunities to measure survival and remotely study the breeding success of wild birds, i.e., by locating nests. This is particularly useful for species whose nests are difficult to find or access, or when disturbances can impact the breeding outcome. We developed and validated, with field data, a framework to detect nesting events by two sandgrouse species, the black-bellied (Pterocles orientalis) and pin-tailed sandgrouse (Pterocles alchata), using GPS and Overall Dynamic Body Acceleration (ODBA) data. Sandgrouses are ground-nesting, cryptic, and elusive birds with biparental incubation efforts. Because both sexes take turns to incubate, a novel framework considering when tagged individuals are on incubation duty or not needs to be designed to detect nests. Results: We tagged 52 birds with high-resolution GPS devices to monitor their breeding during 2021–24. Using remote tracking and field data from the first 2 years (2021–22), we first determined sex-specific time windows for incubation to maximise differentiation between incubation and non-incubation behaviours. We then used a threshold-based classification to identify incubation days and inferred the minimum number of successive incubation days needed to correctly identify a nesting event. We show how ODBA and GPS data can be used to successfully detect nests incubated for only 2 or 3 days. GPS-only data or combined GPS-ODBA data had a success rate of around 95%, whereas ODBA-only data had a success rate of 100%. Cross-validation using data from 2023 to 2024 confirmed the model's performance, showing an overall success > 90% for GPS-only and ODBA-only data and of 85% for combined GPS–ODBA data. Conclusions: By accurately identifying nesting events, our framework offers new opportunities to study the breeding of conservation-dependent species. Besides its applicability to ground-nesting species with biparental care and sex-specific incubation schedules, the framework can be adapted to other bird species sensitive to disturbances or with inaccessible nesting sites. By doing so, it reduces the need for nest visits and associated disturbances, as well as the carbon footprint and expenses associated with fieldwork. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Precision Medicine in Cats: Novel Niemann‐Pick Type C1 Diagnosed by Whole‐Genome Sequencing

Author

Mauler, DA, Gandolfi, B, Reinero, CR, O'Brien, DP, Spooner, JL, Lyons, LA, Aberdein, Danielle, Alves, Paulo C, Barsh, Gregory S, Beale, Holly C, Boyko, Adam R, Brockman, Jeffrey A, Castelhano, Marta G, Chan, Patricia P, Matthew Ellinwood, N, Fogle, Jonathan E, Garrick, Dorian J, Helps, Christopher R, Hytönen, Marjo K, Kaukonen, Maria, Kaelin, Christopher B, Leclerc, Emilie, Leeb, Tosso, Lohi, Hannes, Longeri, Maria, Malik, Richard, Montague, Michael J, Munday, John S, Murphy, William J, Pedersen, Niels C, Rothschild, Max F, Stern, Joshua A, Swanson, William F, Terio, Karen A, Todhunter, Rory J, Ueda, Yu, Warren, Wesley C, Wilcox, Elizabeth A, and Wildschutte, Julia H

Subjects
Genetics, HIV/AIDS, Human Genome, Biotechnology, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Animals, Cat Diseases, Cats, Female, Genome, Niemann-Pick Disease, Type C, Precision Medicine, Sequence Analysis, DNA, and 99 Lives Consortium, Felis silvestris catus, NPC1, WGS, Feline, Lysosomal storage, Veterinary Sciences
Abstract

State-of-the-art health care includes genome sequencing of the patient to identify genetic variants that contribute to either the cause of their malady or variants that can be targeted to improve treatment. The goal was to introduce state-of-the-art health care to cats using genomics and a precision medicine approach. To test the feasibility of a precision medicine approach in domestic cats, a single cat that presented to the University of Missouri, Veterinary Health Center with an undiagnosed neurologic disease was whole-genome sequenced. The DNA variants from the cat were compared to the DNA variant database produced by the 99 Lives Cat Genome Sequencing Consortium. Approximately 25× genomic coverage was produced for the cat. A predicted p.H441P missense mutation was identified in NPC1, the gene causing Niemann-Pick type C1 on cat chromosome D3.47456793 caused by an adenine-to-cytosine transversion, c.1322A>C. The cat was homozygous for the variant. The variant was not identified in any other 73 domestic and 9 wild felids in the sequence database or 190 additionally genotyped cats of various breeds. The successful effort suggested precision medicine is feasible for cats and other undiagnosed cats may benefit from a genomic analysis approach. The 99 Lives DNA variant database was sufficient but would benefit from additional cat sequences. Other cats with the mutation may be identified and could be introduced as a new biomedical model for NPC1. A genetic test could eliminate the disease variant from the population.

Published
2017

32. Eco-physiological arguments on the functional impact of Lepus timidus mitochondrial DNA introgression in Iberian hares (Lepus granatensis)

Author

Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Cardoso, Beatriz, Carpio, Antonio J., Martínez-Haro, Mónica, Beltrán-Beck, Beatriz, Alzaga, Vanesa, Farelo, Liliana, Campos, Rita, Queirós, João, Melo-Ferreira, José, Alves, Paulo C., Acevedo, Pelayo, Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Cardoso, Beatriz, Carpio, Antonio J., Martínez-Haro, Mónica, Beltrán-Beck, Beatriz, Alzaga, Vanesa, Farelo, Liliana, Campos, Rita, Queirós, João, Melo-Ferreira, José, Alves, Paulo C., and Acevedo, Pelayo

Abstract

Genetic exchanges between species provide valuable opportunities to dissect the relative importance of neutral and selective processes driving introgression events and to test their functional relevance. In the northern half of the Iberian Peninsula, the Iberian hare, Lepus granatensis, presents extensive patterns of mitochondrial DNA (mtDNA) introgression from the mountain hare, L. timidus, a species that disappeared from the region after the Last Glacial Maximum. Here, we test whether mtDNA introgression affects reproductive success and body condition of Iberian hare individuals. For that end, hares (n = 149) were sampled from populations along the mtDNA introgression gradient during the 2013–2014 and 2014–2015 hunting seasons. Reproductive performance indicators, including pregnancy status and testicular weight, were recorded, while body condition was measured as kidney fat (our response variables). Predictors included individual traits (sex and age), sampling period (month and hunting season), mtDNA introgression, occurrence or burden of different endoparasites and environmental factors. Our results showed that mtDNA introgression was negatively associated with pregnancy in females and body condition in males, while a positive association was found with body condition in females. These results suggest that carrying the mountain hare mtDNA has physiological effects in Iberian hares, but that the allospecific mtDNA type may not always be beneficial for the individual. This study shows that the patterns of mtDNA introgression seen in the Iberian hare today may result from a complex balance between deleterious and beneficial individual effects.

Published
2024

33. European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Author

Mattucci, Federica, Oliveira, Rita, Lyons, Leslie A, Alves, Paulo C, and Randi, Ettore

Subjects
Biological Sciences, Ecology, Genetics, Life on Land, ABC simulations, Bayesian clustering, conservation genetics, Felis silvestris, microsatellites, phylogeography, population structure, wild and domestic cat hybridization, Evolutionary Biology, Evolutionary biology, Ecological applications
Abstract

Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average Ф ST = 0.159, r st = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average Ф ST = 0.103, r st = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene-early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored.

Published
2016

34. Range-wide patterns of human-mediated hybridisation in European wildcats

Author

Tiesmeyer, Annika, Ramos, Luana, Manuel Lucas, José, Steyer, Katharina, Alves, Paulo C., Astaras, Christos, Brix, Mareike, Cragnolini, Margherita, Domokos, Csaba, Hegyeli, Zsolt, Janssen, René, Kitchener, Andrew C., Lambinet, Clotilde, Mestdagh, Xavier, Migli, Despina, Monterroso, Pedro, Mulder, Jaap L., Schockert, Vinciane, Youlatos, Dionisios, Pfenninger, Markus, and Nowak, Carsten

Published
2020
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35. Feline mitochondrial DNA sampling for forensic analysis: when enough is enough!

Author

Grahn, Robert A, Alhaddad, Hasan, Alves, Paulo C, Randi, Ettore, Waly, Nashwa E, and Lyons, Leslie A

Subjects
Mitochondria, Hair, Animals, Cats, DNA, Mitochondrial, DNA Fingerprinting, Databases, Nucleic Acid, Forensic Genetics, Pets, Control region, Domestic cat, Felis silvestris catus, Forensic Science, Mitotype, mtDNA, HIV/AIDS, Genetics, Mathematical Sciences, Biological Sciences, Law and Legal Studies, Legal & Forensic Medicine
Abstract

Pet hair has a demonstrated value in resolving legal issues. Cat hair is chronically shed and it is difficult to leave a home with cats without some level of secondary transfer. The power of cat hair as an evidentiary resource may be underused because representative genetic databases are not available for exclusionary purposes. Mitochondrial control region databases are highly valuable for hair analyses and have been developed for the cat. In a representative worldwide data set, 83% of domestic cat mitotypes belong to one of twelve major types. Of the remaining 17%, 7.5% are unique within the published 1394 sample database. The current research evaluates the sample size necessary to establish a representative population for forensic comparison of the mitochondrial control region for the domestic cat. For most worldwide populations, randomly sampling 50 unrelated local individuals will achieve saturation at 95%. The 99% saturation is achieved by randomly sampling 60-170 cats, depending on the numbers of mitotypes available in the population at large. Likely due to the recent domestication of the cat and minimal localized population substructure, fewer cats are needed to meet mitochondria DNA control region database practical saturation than for humans or dogs. Coupled with the available worldwide feline control region database of nearly 1400 cats, minimal local sampling will be required to establish an appropriate comparative representative database and achieve significant exclusionary power.

Published
2015

39. Eco‐physiological arguments on the functional impact of Lepus timidus mitochondrial DNA introgression in Iberian hares (Lepus granatensis).

Author

Cardoso, Beatriz, Carpio, Antonio J., Martinez‐Haro, Mónica, Beltrán‐Beck, Beatriz, Alzaga, Vanesa, Farelo, Liliana, Campos, Rita, Queirós, João, Melo‐Ferreira, José, Alves, Paulo C., and Acevedo, Pelayo

Subjects
INTROGRESSION (Genetics), MITOCHONDRIAL DNA, LAST Glacial Maximum, HARES, BIOLOGICAL fitness
Abstract

Genetic exchanges between species provide valuable opportunities to dissect the relative importance of neutral and selective processes driving introgression events and to test their functional relevance. In the northern half of the Iberian Peninsula, the Iberian hare, Lepus granatensis, presents extensive patterns of mitochondrial DNA (mtDNA) introgression from the mountain hare, L. timidus, a species that disappeared from the region after the Last Glacial Maximum. Here, we test whether mtDNA introgression affects reproductive success and body condition of Iberian hare individuals. For that end, hares (n = 149) were sampled from populations along the mtDNA introgression gradient during the 2013–2014 and 2014–2015 hunting seasons. Reproductive performance indicators, including pregnancy status and testicular weight, were recorded, while body condition was measured as kidney fat (our response variables). Predictors included individual traits (sex and age), sampling period (month and hunting season), mtDNA introgression, occurrence or burden of different endoparasites and environmental factors. Our results showed that mtDNA introgression was negatively associated with pregnancy in females and body condition in males, while a positive association was found with body condition in females. These results suggest that carrying the mountain hare mtDNA has physiological effects in Iberian hares, but that the allospecific mtDNA type may not always be beneficial for the individual. This study shows that the patterns of mtDNA introgression seen in the Iberian hare today may result from a complex balance between deleterious and beneficial individual effects. [ABSTRACT FROM AUTHOR]

Published
2024
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40. 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, additional, Derks, Martijn FL, additional, Diroma, Maria Angela, additional, Djan, Mihajla, additional, Duprat, Simone, additional, Eleftheriadi, Klara, additional, Feulner, Philine GD, additional, Flot, Jean-Francois, additional, Forni, Giobbe, additional, Fosso, Bruno, additional, Fournier, Pascal, additional, Fournier-Chambrillon, Christine, additional, Gabaldon, Toni, additional, Garg, Shilpa, additional, Gissi, Carmela, additional, Giupponi, Luca, additional, Gomez-Garrido, Jessica, additional, Gonzalez, Josefa, additional, Grilo, Miguel L, additional, Gruening, Bjoern, additional, Guerin, Thomas, additional, Guiglielmoni, Nadege, additional, Gut, Marta, additional, Haesler, Marcel P, additional, Hahn, Christoph, additional, Halpern, Balint, additional, Harrison, Peter, additional, Heintz, Julia, additional, Hindrikson, Maris, additional, Hoglund, Jacob, additional, Howe, Kerstin, additional, Hughes, Graham, additional, Istace, Benjamin, additional, Cock, Mark J., additional, Jancekovic, Franc, additional, Jonsson, Zophonias O, additional, Joye-Dind, Sagane, additional, Koskimaki, Janne J., additional, Krystufek, Boris, additional, Kubacka, Justyna, additional, Kuhl, Heiner, additional, Kusza, Szilvia, additional, Labadie, Karine, additional, Lahteenaro, Meri, additional, Lantz, Henrik, additional, Lavrinienko, Anton, additional, Leclere, Lucas, additional, Lopes, Ricardo Jorge, additional, Madsen, Ole, additional, Magdelenat, Ghislaine, additional, Magoga, Giulia, additional, Manousaki, Tereza, additional, Mappes, Tapio, additional, Marques, Joao Pedro, additional, Martinez Redondo, Gemma I, additional, Maumus, Florian, additional, Megens, Hendrik-Jan, additional, Melo-Ferreira, Jose, additional, Mendes, Sofia L, additional, Montagna, Matteo, additional, Moreno, Joao, additional, Mosbech, Mai-Britt, additional, Moura, Monica, additional, Musilova, Zuzana, additional, Myers, Eugene, additional, Nash, Will J., additional, Nater, Alexander, additional, Nicholson, Pamela, additional, Niell, Manuel, additional, Nijland, Reindert, additional, Noel, Benjamin, additional, Noren, Karin, additional, Oliveira, Pedro H, additional, Olsen, Remi-Andre, additional, Ometto, Lino, additional, Ossowski, Stephan, additional, Palinauskas, Vaidas, additional, Palsson, Snaebjorn, additional, Panibe, Jerome P, additional, Pauperio, Joana, additional, Pavlek, Martina, additional, Payen, Emilie, additional, Pawlowska, Julia, additional, Pellicer, Jaume, additional, Pesole, Graziano, additional, Pimenta, Joao, additional, Pippel, Martin, additional, Pirttila, Anna Maria, additional, Poulakakis, Nikos, additional, Rajan, Jeena, additional, Rego, Ruben MC, additional, Resendes, Roberto, additional, Resl, Philipp, additional, Riesgo, Ana, additional, Rodin-Morch, Patrik, additional, Soares, Andre ER, additional, Rodriguez Fernandes, Carlos, additional, Romeiras, Maria M., additional, Roxo, Guilherme, additional, Ruber, Lukas, additional, Ruiz-Lopez, Maria Jose, additional, Saarma, Urmas, additional, Silva, Luis P, additional, Sim-Sim, Manuela, additional, Soler, Lucile, additional, Sousa, Vitor C, additional, Sousa Santos, Carla, additional, Spada, Alberto, additional, Stefanovic, Milomir, additional, Steger, Viktor, additional, Stiller, Josefin, additional, Stock, Matthias, additional, Struck, Torsten Hugo H, additional, Sudasinghe, Hiranya, additional, Tapanainen, Riikka, additional, Tellgren-Roth, Christian, additional, Trindade, Helena, additional, Tukalenko, Yevhen, additional, Urso, Ilenia, additional, Vacherie, Benoit, additional, Van Belleghem, Steven M, additional, van Oers, Kees, additional, Vargas-Chavez, Carlos, additional, Velickovic, Nevena, additional, Vella, Noel, additional, Vella, Adriana, additional, Vernesi, Cristiano, additional, Vicente, Sara, additional, Villa, Sara, additional, Vinnere Pettersson, Olga, additional, Volckaert, Filip AM, additional, Voros, Judit, additional, Wincker, Patrick, additional, and Winkler, Sylke, additional

Published
2023
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43. How genomics can help biodiversity conservation

Author

Theissinger, Kathrin, primary, Fernandes, Carlos, additional, Formenti, Giulio, additional, Bista, Iliana, additional, Berg, Paul R., additional, Bleidorn, Christoph, additional, Bombarely, Aureliano, additional, Crottini, Angelica, additional, Gallo, Guido R., additional, Godoy, José A., additional, Jentoft, Sissel, additional, Malukiewicz, Joanna, additional, Mouton, Alice, additional, Oomen, Rebekah A., additional, Paez, Sadye, additional, Palsbøll, Per J., additional, Pampoulie, Christophe, additional, Ruiz-López, María J., additional, Secomandi, Simona, additional, Svardal, Hannes, additional, Theofanopoulou, Constantina, additional, de Vries, Jan, additional, Waldvogel, Ann-Marie, additional, Zhang, Guojie, additional, Jarvis, Erich D., additional, Bálint, Miklós, additional, Ciofi, Claudio, additional, Waterhouse, Robert M., additional, Mazzoni, Camila J., additional, Höglund, Jacob, additional, Aghayan, Sargis A., additional, Alioto, Tyler S., additional, Almudi, Isabel, additional, Alvarez, Nadir, additional, Alves, Paulo C., additional, Amorim do Rosario, Isabel R., additional, Antunes, Agostinho, additional, Arribas, Paula, additional, Baldrian, Petr, additional, Bertorelle, Giorgio, additional, Böhne, Astrid, additional, Bonisoli-Alquati, Andrea, additional, Boštjančić, Ljudevit L., additional, Boussau, Bastien, additional, Breton, Catherine M., additional, Buzan, Elena, additional, Campos, Paula F., additional, Carreras, Carlos, additional, Castro, L. FIlipe C., additional, Chueca, Luis J., additional, Čiampor, Fedor, additional, Conti, Elena, additional, Cook-Deegan, Robert, additional, Croll, Daniel, additional, Cunha, Mónica V., additional, Delsuc, Frédéric, additional, Dennis, Alice B., additional, Dimitrov, Dimitar, additional, Faria, Rui, additional, Favre, Adrien, additional, Fedrigo, Olivier D., additional, Fernández, Rosa, additional, Ficetola, Gentile Francesco, additional, Flot, Jean-François, additional, Gabaldón, Toni, additional, Agius, Dolores R., additional, Giani, Alice M., additional, Gilbert, M. Thomas P., additional, Grebenc, Tine, additional, Guschanski, Katerina, additional, Guyot, Romain, additional, Hausdorf, Bernhard, additional, Hawlitschek, Oliver, additional, Heintzman, Peter D., additional, Heinze, Berthold, additional, Hiller, Michael, additional, Husemann, Martin, additional, Iannucci, Alessio, additional, Irisarri, Iker, additional, Jakobsen, Kjetill S., additional, Klinga, Peter, additional, Kloch, Agnieszka, additional, Kratochwil, Claudius F., additional, Kusche, Henrik, additional, Layton, Kara K.S., additional, Leonard, Jennifer A., additional, Lerat, Emmanuelle, additional, Liti, Gianni, additional, Manousaki, Tereza, additional, Marques-Bonet, Tomas, additional, Matos-Maraví, Pável, additional, Matschiner, Michael, additional, Maumus, Florian, additional, Mc Cartney, Ann M., additional, Meiri, Shai, additional, Melo-Ferreira, José, additional, Mengual, Ximo, additional, Monaghan, Michael T., additional, Montagna, Matteo, additional, Mysłajek, Robert W., additional, Neiber, Marco T., additional, Nicolas, Violaine, additional, Novo, Marta, additional, Ozretić, Petar, additional, Palero, Ferran, additional, Pârvulescu, Lucian, additional, Pascual, Marta, additional, Paulo, Octávio S., additional, Pavlek, Martina, additional, Pegueroles, Cinta, additional, Pellissier, Loïc, additional, Pesole, Graziano, additional, Primmer, Craig R., additional, Riesgo, Ana, additional, Rüber, Lukas, additional, Rubolini, Diego, additional, Salvi, Daniele, additional, Seehausen, Ole, additional, Seidel, Matthias, additional, Studer, Bruno, additional, Theodoridis, Spyros, additional, Thines, Marco, additional, Urban, Lara, additional, Vasemägi, Anti, additional, Vella, Adriana, additional, Vella, Noel, additional, Vernes, Sonja C., additional, Vernesi, Cristiano, additional, Vieites, David R., additional, Wheat, Christopher W., additional, Wörheide, Gert, additional, Wurm, Yannick, additional, and Zammit, Gabrielle, additional

Published
2023
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45. The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates

Author

Ferreira, Mafalda S., primary, Thurman, Timothy J., additional, Jones, Matthew R., additional, Farelo, Liliana, additional, Kumar, Alexander V., additional, Mortimer, Sebastian M. E., additional, Demboski, John R., additional, Mills, L. Scott, additional, Alves, Paulo C., additional, Melo-Ferreira, José, additional, and Good, Jeffrey M., additional

Published
2023
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46. Normalised absorbance ratios of IgG for myxoma and rabbit hemorrhagic disease viruses: Longitudinal dataset wild European rabbits

Author

Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Junta de Comunidades de Castilla-La Mancha, Ministerio de Universidades (España), Santos, Nuno, Coelho, Joana, Pacheco, Henrique, Rafael, Marta, Jiménez-Ruiz, Saúl, Alves, Paulo C., Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Junta de Comunidades de Castilla-La Mancha, Ministerio de Universidades (España), Santos, Nuno, Coelho, Joana, Pacheco, Henrique, Rafael, Marta, Jiménez-Ruiz, Saúl, and Alves, Paulo C.

Abstract

This study addresses the long-term dynamics of humoral immunity to two viral pathogens of the European rabbit, an endangered keystone species of major ecological relevance. Such studies are particularly challenging in free-ranging species, and a combination of longitudinal capture-mark-recapture and semi-quantitative serology was used to address this question. Over 600 normalised absorbance ratios of indirect ELISA, obtained from 505 individual rabbits in 7 populations over five years were analysed using linear mixed models. The results support a lifelong acquired humoral immunity to myxoma virus and rabbit hemorrhagic disease virus upon natural infection and suggest the presence of maternal immunity to the latter in wild juvenile rabbits. These results contribute to understanding the epidemiology of two viral diseases threatening this keystone species and assist in developing conservation programs.

Published
2023

47. Dynamics of humoral immunity to myxoma and rabbit hemorrhagic disease viruses in wild european rabbits assessed by longitudinal semiquantitative serology

Author

Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Comissão de Coordenação e Desenvolvimento Regional do Norte (Portugal), Universidad de Castilla La Mancha, Ministerio de Universidades (España), Coelho, Joana, Pacheco, Henrique, Rafael, Marta, Jiménez-Ruiz, Saúl, Alves, Paulo C., Santos, Nuno, Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Comissão de Coordenação e Desenvolvimento Regional do Norte (Portugal), Universidad de Castilla La Mancha, Ministerio de Universidades (España), Coelho, Joana, Pacheco, Henrique, Rafael, Marta, Jiménez-Ruiz, Saúl, Alves, Paulo C., and Santos, Nuno

Abstract

Myxoma virus (MYXV) and rabbit hemorrhagic disease virus (RHDV) are important drivers of the population decline of the European rabbit, an endangered keystone species. Both viruses elicit strong immune responses, but the long-term dynamics of humoral immunity are imperfectly known. This study aimed to assess the determinants of the long-term dynamics of antibodies to each virus based on a longitudinal capture-mark-recapture of wild European rabbits and semiquantitative serological data of MYXV and RHDV GI.2-specific IgG. The study included 611 indirect enzyme-linked immunosorbent assay (iELISA) normalized absorbance ratios for each MYXV and RHDV GI.2 from 505 rabbits from 2018 to 2022. Normalized absorbance ratios were analyzed using log-linear mixed models, showing a significant positive relationship with the time since the first capture of individual rabbits, with monthly increases of 4.1% for antibodies against MYXV and 2.0% against RHDV GI.2. Individual serological histories showed fluctuations over time, suggesting that reinfections boosted the immune response and likely resulted in lifelong immunity. Normalized absorbance ratios significantly increased with the seroprevalence in the population, probably because of recent outbreaks, and with body weight, highlighting the role of MYXV and RHDV GI.2 in determining survival to adulthood. Juvenile rabbits seropositive for both viruses were found, and the dynamics of RHDV GI.2 normalized absorbance ratios suggest the presence of maternal immunity up to 2 months of age. Semiquantitative longitudinal serological data provide epidemiological information, otherwise lost when considering only qualitative data, and support a lifelong acquired humoral immunity to RHDV GI.2 and MYXV upon natural infection., [Importance] This study addresses the long-term dynamics of humoral immunity to two major viral pathogens of the European rabbit, an endangered keystone species of major ecological relevance. Such studies are particularly challenging in free-ranging species, and a combination of longitudinal capture-mark-recapture and semiquantitative serology was used to address this question. Over 600 normalized absorbance ratios of iELISA, obtained from 505 individual rabbits in 7 populations over 5 years, were analyzed using linear mixed models. The results support a lifelong acquired humoral immunity to myxoma virus and rabbit hemorrhagic disease virus upon natural infection and suggest the presence of maternal immunity to the latter in wild juvenile rabbits. These results contribute to understanding the epidemiology of two viral diseases threatening this keystone species and assist in developing conservation programs.

Published
2023

48. Supplementary material for Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants

Author

Rajbhandari, Rajesh Man, Napit, Rajindra, Manandhar, Prajwol, Raut, Roji, Gurung, Anupama, Poudel, Ajit, Shrestha, Nisha, Sadaula, Amir, Karmacharya, Dibesh, Gortázar, Christian, Alves, Paulo C., Fuente, José de la, Queirós, João, Rajbhandari, Rajesh Man, Napit, Rajindra, Manandhar, Prajwol, Raut, Roji, Gurung, Anupama, Poudel, Ajit, Shrestha, Nisha, Sadaula, Amir, Karmacharya, Dibesh, Gortázar, Christian, Alves, Paulo C., Fuente, José de la, and Queirós, João

Published
2023

49. Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants

Author

Fundação para a Ciência e a Tecnologia (Portugal), Rajbhandari, Rajesh Man, Napit, Rajindra, Manandhar, Prajwol, Raut, Roji, Gurung, Anupama, Poudel, Ajit, Shrestha, Nisha, Sadaula, Amir, Karmacharya, Dibesh, Gortázar, Christian, Alves, Paulo C., Fuente, José de la, Queirós, João, Fundação para a Ciência e a Tecnologia (Portugal), Rajbhandari, Rajesh Man, Napit, Rajindra, Manandhar, Prajwol, Raut, Roji, Gurung, Anupama, Poudel, Ajit, Shrestha, Nisha, Sadaula, Amir, Karmacharya, Dibesh, Gortázar, Christian, Alves, Paulo C., Fuente, José de la, and Queirós, João

Abstract

[Introduction]: Tuberculosis is an infectious disease caused by a group of acid-fast bacilli known as Mycobacterium tuberculosis complex (MTC), which has a major impact on humans. Transmission of MTC across the human-animal interface has been demonstrated by several studies. However, the reverse zoonotic transmission from humans to animals (zooanthroponosis) has often been neglected., [Methods]: In this study, we used Nanopore MinION and Illumina MiSeq approaches to sequence the whole genome of M. tuberculosis strains isolated from two deceased Asian elephants (Elephas maximus) and one human in Chitwan, Nepal. The evolutionary relationships and drug resistance capacity of these strains were assessed using the whole genome data generated by the stand-alone tool Tb-Profiler. Phylogenomic trees were also constructed using a non-synonymous SNP alignment of 2,596 bp, including 94 whole genome sequences representative of the previously described M. tuberculosis lineages from elephants worldwide (lineages 1 and 4) and from humans in Nepal (lineages 1, 2 and 3)., [Results and discussion]: The new genomes achieved an average coverage of 99.6%, with an average depth of 55.67x. These M. tuberculosis strains belong to lineage 1 (elephant DG), lineage 2 (elephant PK) and lineage 4 (human), and none of them were found to have drug-resistant variants. The elephant-derived isolates were evolutionarily closely related to human-derived isolates previously described in Nepal, both in lineages 1 and 2, providing additional support for zooanthroponosis or bidirectional transmission between humans and elephants. The human-derived isolate clustered together with other published human isolates from Argentina, Russia and the United Kingdom in the lineage 4 clade. This complex multi-pathogen, multi-host system is challenging and highlights the need for a One Health approach to tuberculosis prevention and control at human-animal interface, particularly in regions where human tuberculosis is highly endemic.

Published
2023

50. Understanding the impact of wild boar on the European wild rabbit and red-legged partridge populations using a diet metabarcoding approach

Author

Consejo Superior de Investigaciones Científicas (España), Conferencia de Rectores de las Universidades Españolas, Universidad de Castilla La Mancha, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Carpio, Antonio J., Queirós, João, Laguna, Eduardo, Jiménez-Ruiz, Saúl, Vicente, Joaquín, Alves, Paulo C., Acevedo, Pelayo, Consejo Superior de Investigaciones Científicas (España), Conferencia de Rectores de las Universidades Españolas, Universidad de Castilla La Mancha, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Carpio, Antonio J., Queirós, João, Laguna, Eduardo, Jiménez-Ruiz, Saúl, Vicente, Joaquín, Alves, Paulo C., and Acevedo, Pelayo

Abstract

European wild rabbit (Oryctolagus cuniculus) and red-legged partridge (Alectoris rufa) are main small game species of conservation concern in Mediterranean ecosystems. To date, their presence in wild boar’s (Sus scrofa) diet and factors driving their consumption have been little investigated. A genetic metabarcoding approach was used on 80 wild boar faeces collected from four hunting estates devoted to small game hunting during two different seasons. Abundances of wild boar, rabbits and partridges were first estimated. Results showed DNA of seventeen chordate species. The highest frequency of occurrence (FO) corresponded to mammals and birds, with 77.6 and 22.3%, respectively. DNA of game species was detected in 39/71 (FO = 55.0%) samples, highlighting the presence of European wild rabbit in 27 (FO = 38.0%) and red-legged partridge in eight (FO = 11.3%). Dietary composition varied between seasons and estates, being rabbit the main responsible (explaining 35.26% and 39.45% of differences, respectively). Rabbit FO in the diet was positively related to the abundance of wild boar and rabbit density on the estate. It was greater in autumn and in estates where rabbits were hunted. Regarding red-legged partridge, a significant and positive relationship between its population density and its diet FO was observed, without significant differences between seasons or estates. Overall, our results suggest wild boar as an opportunistic species whose diet is largely determined by the relative availability of different food resources. Its ecological role concerning small game species in Mediterranean agroecosystems seems to be more related to consumption of carrion during the hunting season than to direct predation.

Published
2023

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