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256 results on '"Melo‐Ferreira, José"'

1. 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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5. How genomics can help biodiversity conservation

Author

Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim do Rosario, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, 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 C., Chueca, Luis J., Čiampor, Fedor, 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, Agius, Dolores 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., 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, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, José A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Bálint, Miklós, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., and Höglund, Jacob

Published
2023
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8. 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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9. 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

11. The genomic architecture of population divergence between subspecies of the European rabbit.

Author

Carneiro, Miguel, Albert, Frank, Afonso, Sandra, Pereira, Ricardo, Burbano, Hernan, Campos, Rita, Melo-Ferreira, José, Blanco-Aguiar, Jose, Villafuerte, Rafael, Nachman, Michael, Good, Jeffrey, and Ferrand, Nuno

Subjects
Animals, Centromere, Europe, Gene Flow, Genetic Speciation, Genetics, Population, Genomics, High-Throughput Nucleotide Sequencing, Hybridization, Genetic, Mice, Rabbits, Reproductive Isolation, X Chromosome
Abstract

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In this study, we used next-generation sequencing to study genome-wide patterns of genetic differentiation between two hybridizing subspecies of rabbits (Oryctolagus cuniculus algirus and O. c. cuniculus) that are known to undergo high rates of gene exchange. Our primary objective was to identify specific genes or genomic regions that have resisted introgression and are likely to confer reproductive barriers in natural conditions. On the basis of 326,000 polymorphisms, we found low to moderate overall levels of differentiation between subspecies, and fewer than 200 genomic regions dispersed throughout the genome showing high differentiation consistent with a signature of reduced gene flow. Most differentiated regions were smaller than 200 Kb and contained very few genes. Remarkably, 30 regions were each found to contain a single gene, facilitating the identification of candidate genes underlying reproductive isolation. This gene-level resolution yielded several insights into the genetic basis and architecture of reproductive isolation in rabbits. Regions of high differentiation were enriched on the X-chromosome and near centromeres. Genes lying within differentiated regions were often associated with transcription and epigenetic activities, including chromatin organization, regulation of transcription, and DNA binding. Overall, our results from a naturally hybridizing system share important commonalities with hybrid incompatibility genes identified using laboratory crosses in mice and flies, highlighting general mechanisms underlying the maintenance of reproductive barriers.

Published
2014

17. 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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19. 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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20. Evolutionary and functional characterization of lagomorph guanylate-binding proteins: a story of gain and loss and shedding light on expression, localization and innate immunity-related functions.

Author

Schelle, Luca, Vasco Côrte-Real, João, Fayyaz, Sharmeen, del Pozo Ben, Augusto, Shnipova, Margarita, Petersen, Moritz, Lotke, Rishikesh, Menon, Bhavna, Matzek, Dana, Pfaff, Lena, Pinheiro, Ana, Pedro Marques, João, Melo-Ferreira, José, Popper, Bastian, José Esteves, Pedro, Sauter, Daniel, Abrantes, Joana, and Baldauf, Hanna-Mari

Subjects
GENE expression, REVERSE transcriptase polymerase chain reaction, LAGOMORPHA, EUROPEAN rabbit, HISTOCOMPATIBILITY class I antigens, PENTRAXINS, CARRIER proteins
Abstract

Guanylate binding proteins (GBPs) are an evolutionarily ancient family of proteins that are widely distributed among eukaryotes. They belong to the dynamin superfamily of GTPases, and their expression can be partially induced by interferons (IFNs). GBPs are involved in the cell-autonomous innate immune response against bacterial, parasitic and viral infections. Evolutionary studies have shown that GBPs exhibit a pattern of gene gain and loss events, indicative for the birth-and-death model of evolution. Most species harbor large GBP gene clusters that encode multiple paralogs. Previous functional and in-depth evolutionary studies have mainly focused on murine and human GBPs. Since rabbits are another important model system for studying human diseases, we focus here on lagomorphs to broaden our understanding of the multifunctional GBP protein family by conducting evolutionary analyses and performing a molecular and functional characterization of rabbit GBPs. We observed that lagomorphs lack GBP3, 6 and 7. Furthermore, Leporidae experienced a loss of GBP2, a unique duplication of GBP5 and a massive expansion of GBP4. Gene expression analysis by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and transcriptome data revealed that leporid GBP expression varied across tissues. Overexpressed rabbit GBPs localized either uniformly and/or discretely to the cytoplasm and/or to the nucleus. Oryctolagus cuniculus (oc)GBP5L1 and rarely ocGBP5L2 were an exception, colocalizing with the trans-Golgi network (TGN). In addition, four ocGBPs were IFN-inducible and only ocGBP5L2 inhibited furin activity. In conclusion, from an evolutionary perspective, lagomorph GBPs experienced multiple gain and loss events, and the molecular and functional characteristics of ocGBP suggest a role in innate immunity. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha: Leporidae).

Author

Costa, José, Queirós, João, Ballesteros, Fernando, Mucci, Nadia, Souto, João, Silva, Eugénio, Melo-Ferreira, José, and Alves, Paulo Célio

Subjects
GENETIC variation, INTROGRESSION (Genetics), LAGOMORPHA, POPULATION differentiation, HARES, ENDANGERED species, MICROSATELLITE repeats, CYTOCHROME c
Abstract

The broom hare (Lepus castroviejoi) is a threatened Iberian endemic, for which there is limited knowledge. We use genetic non-invasive sampling (gNIS; N  = 185 faeces samples) and specimens from hunting and roadkills (N  = 22) in conjunction with a 15-microsatellite panel and a 541-bp fragment of cytochrome- b to assess the genetic diversity, population structure and evolutionary history of this species. Populations from the other four European hare species were also analysed to accurately compare the genetic diversity patterns and infer admixture. Species identification from gNIS was inferred using small fragments of cytochrome- b and transferrin genes and individual identification was obtained using microsatellites. The broom hare population showed the lowest level of nuclear DNA diversity of all analysed hare species (N  = 76; Na  = 2.53, H e = 0.186 and F is = 0.341) and very low mitochondrial DNA diversity (N  = 64; H d = 0.743 and π = 0.01543). Only the Italian hare (L. corsicanus) showed a similar pattern of low genetic diversity. No hybridization with the neighbouring hare species was detected. However, two mitochondrial DNA lineages, corresponding to two ancient events of introgression of mountain hare (L. timidus) origin, were characterized. There was evidence for shallow spatial population differentiation of the broom hare. The described reduced genetic diversity, associated with a narrow distribution range and recent population declines, represents a risk of population extinction, and highlights the need for conservation measures of this endemic threatened hare species. [ABSTRACT FROM AUTHOR]

Published
2024
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22. Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection

Author

Böhne, Astrid, primary, Fernández, Rosa, additional, Leonard, Jennifer A., additional, McCartney, Ann M., additional, McTaggart, Seanna, additional, Melo-Ferreira, José, additional, Monteiro, Rita, additional, Oomen, Rebekah A., additional, Pettersson, Olga Vinnere, additional, and Struck, Torsten H., additional

Published
2023
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24. Iberian Hare Lepus granatensis Rosenhauer, 1856

Author

Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Ciencia e Innovación (España), European Commission, Agencia Estatal de Investigación (España), Fundação para a Ciência e a Tecnologia (Portugal), Alves, Paulo C., Acevedo, Pelayo, Melo-Ferreira, José, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Ciencia e Innovación (España), European Commission, Agencia Estatal de Investigación (España), Fundação para a Ciência e a Tecnologia (Portugal), Alves, Paulo C., Acevedo, Pelayo, and Melo-Ferreira, José

Abstract

This comprehensive species-specific chapter covers all aspects of the mammalian biology, including paleontology, physiology, genetics, reproduction and development, ecology, habitat, diet, mortality, and behavior. The economic significance and management of mammals and future challenges for research and conservation are addressed as well. The chapter includes a distribution map, a photograph of the animal, and a list of key literature.

Published
2023

26. 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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36. The evolutionary pathways for local adaptation in mountain hares

Author

Giska, Iwona, primary, Pimenta, João, additional, Farelo, Liliana, additional, Boursot, Pierre, additional, Hackländer, Klaus, additional, Jenny, Hannes, additional, Reid, Neil, additional, Montgomery, W. Ian, additional, Prodöhl, Paulo A., additional, Alves, Paulo C., additional, and Melo‐Ferreira, José, additional

Published
2022
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38. Let's talk about climate change... but when do we start?

Author

Campos, Rita and Melo-Ferreira, José

Abstract

Climate change poses numerous challenges to the environment and the survival of species, humans included. But in spite of the scientific consensus related to the influence of human activities on environmental imbalance, and the recent civic mobilization demanding political action to address climate change, there is still some resistance on the public opinion about the real impacts of the current climate crisis. Science communication can be a powerful ally to raise awareness on these issues. “Coats for snow” is an activity to help communicating the impacts of climate change and foster new dialogues on the topic. It was designed as a “consultative science communication” activity, inspired by the “AEIOU vowel analogy” of science communication. As such, to facilitate Interest and Understanding, we tell a story inspired on ongoing research, studying how species adapted to cold environments with winter snow can be affected by increasing global temperature and consequent decrease of snow cover. To promote engagement and Enjoyment, we use a game that allows the active participation of the public. To contribute to informed Opinions and behavioural changes, we include a before-and-after debate, where different aspects of climate change can be addressed. The activity was tested with children aged 9-10 years old after a guided visit to a Natural History Museum Gallery. It proved to be an attractive strategy, encouraging highly interactive discussions around climate change and its impact on biodiversity. However, even though climate change is widely mentioned in the media and many school students are adhering to climate strikes worldwide, almost all children that participated in the activity declared that they have never heard of it. This led us to conclude that efforts to communicate and engage the public with climate change issues should include younger children. Results from the “coats for snow” activity show that it is possible.

Published
2021

39. The evolutionary pathways for local adaptation in mountain hares

Author

Giska, Iwona, primary, Pimenta, João, additional, Farelo, Liliana, additional, Boursot, Pierre, additional, Hackländer, Klaus, additional, Jenny, Hannes, additional, Reid, Neil, additional, Montgomery, W. Ian, additional, Prodöhl, Paulo A., additional, Alves, Paulo C., additional, and Melo-Ferreira, José, additional

Published
2021
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40. Iberian hares with anciently introgressed mitochondrial DNA express a marginal environmental niche

Author

Fundação para a Ciência e a Tecnologia (Portugal), Comissão de Coordenação e Desenvolvimento Regional do Norte (Portugal), European Commission, Universidad de Castilla La Mancha, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Junta de Comunidades de Castilla-La Mancha, Carpio, Antonio J., Melo-Ferreira, José, Martínez-Haro, Mónica, Farelo, Liliana, Campos, Rita, Alves, Paulo C., Acevedo, Pelayo, Fundação para a Ciência e a Tecnologia (Portugal), Comissão de Coordenação e Desenvolvimento Regional do Norte (Portugal), European Commission, Universidad de Castilla La Mancha, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Junta de Comunidades de Castilla-La Mancha, Carpio, Antonio J., Melo-Ferreira, José, Martínez-Haro, Mónica, Farelo, Liliana, Campos, Rita, Alves, Paulo C., and Acevedo, Pelayo

Abstract

[Aim]: The role of mitochondrial DNA (mtDNA) in local adaptation has been thoroughly debated, and the ancient pervasive mtDNA introgression from Lepus timidus into Lepus granatensis allows testing of this hypothesis. Here, we study the environmental niche of animals with introgressed mtDNA, to gain insights about the potential selective pressures maintaining the introgressed haplotypes., [Location]: Iberian Peninsula., [Taxon]: Lepus granatensis., [Methods]: We modelled the frequency of the L. timidus mtDNA lineage within the L. granatensis distribution area. The response variable was the presence of the L. timidus lineage at the individual level. Finally, the variation in the introgression frequencies was plotted along the environmental gradients (identified by the models), after controlling for latitude., [Results]: The results showed that (i) the niche of the introgressed populations occupy marginal environmental conditions relative to the complete niche of L. granatensis, (ii) both latitude and environment, and their overlaid effects, explain the variation in the introgression frequencies, and (iii) after controlling for latitude, clines in mtDNA introgression frequency are associated with transitions in the environmental gradients, even when the analyses were restricted to the territory where the introgressed haplotypes occur., [Main Conclusions]: While the strict demographic explanation for mtDNA introgression in L. granatensis implies that geography, resulting from the post-glacial expansion of the species, explains the gradients of introgression, our results show correlations with environmental gradients that are not geographically structured. Our results relate the prevalence of introgressed mtDNA with more extreme climatic conditions in the range of L. granatensis, suggesting that environmental selective pressures could have played a role in determining the spatial maintenance of mtDNA haplotypes originating from the cold-adapted species. These results are thus relevant to understand the response of the species to the ongoing processes of global change, which will alter the selective pressures by reducing the specific niche of the introgressed mtDNA lineage.

Published
2021

45. Additional file 2 of Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Author

Lado, Sara, Elbers, Jean P., Rogers, Mark F., Melo-Ferreira, José, Yadamsuren, Adiya, Corander, Jukka, Horin, Petr, and Burger, Pamela A.

Subjects
endocrine system
Abstract

Additional file 2: Supplemental Table 2. Means with 95% bootstrap confidence limits (CL, see Methods) of nucleotide diversity for alignments made with non-synonymous and synonymous SNPs and indels and only non-synonymous SNPs in HC (heavy-chain) immunoglobulin genes in DC (domestic camel), DROM (dromedary), and WC (wild camel).

Published
2020
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46. Additional file 1 of Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Author

Lado, Sara, Elbers, Jean P., Rogers, Mark F., Melo-Ferreira, José, Yadamsuren, Adiya, Corander, Jukka, Horin, Petr, and Burger, Pamela A.

Abstract

Additional file 1: Supplemental Table 1. Assembly statistics for the CamFer2 and the Camelus ferus genome (new-CamFer) assembly from Ming et al. (2020b) using a genome size of 2.1 Gbp.

Published
2020
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47. Additional file 5 of Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Author

Lado, Sara, Elbers, Jean P., Rogers, Mark F., Melo-Ferreira, José, Yadamsuren, Adiya, Corander, Jukka, Horin, Petr, and Burger, Pamela A.

Abstract

Additional file 5: Supplemental Figure 3. Means with 95% bootstrap confidence intervals (see Methods) of nucleotide diversity for alignments made with non-synonymous and synonymous SNPs and indels (a) and only non-synonymous SNPs (b): MHC class I and II genes (top panel), innate (second panel), adaptive (third panel), and the rest of genome genes (bottom panel) for: DROM (dromedary, C. dromedarius), DC (domestic Bactrian camel, C. bactrianus), and WC (wild camel, C. ferus). Uppercase letters above upper 95% confidence limits indicate groups have different (non-matching letters) or not different (matching letters) means based on non-overlapping confidence intervals.

Published
2020
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48. Additional file 4 of Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Author

Lado, Sara, Elbers, Jean P., Rogers, Mark F., Melo-Ferreira, José, Yadamsuren, Adiya, Corander, Jukka, Horin, Petr, and Burger, Pamela A.

Abstract

Additional file 4: Supplemental Figure 2. D-GENIES (Cabanettes & Klopp, 2018) dot plot made with Minimap2 [68] whole-genome alignment between CamFer2 and the Camelus ferus genome (new-CamFer) assembly from Ming et al., [12]. Contigs are sorted and matches are filtered using the strong precision setting in D-GENIES.

Published
2020
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49. Additional file 6 of Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Author

Lado, Sara, Elbers, Jean P., Rogers, Mark F., Melo-Ferreira, José, Yadamsuren, Adiya, Corander, Jukka, Horin, Petr, and Burger, Pamela A.

Abstract

Additional file 6: Supplemental Figure 4. Means with 95% bootstrap confidence intervals (see Methods) of nucleotide diversity for alignments made with (left) non-synonymous SNPs, (right) all SNPs and indels in HC (heavy-chain) antibody (immunoglobulin) genes in DC (domestic camel), DROM (dromedary), and WC (wild camel). Uppercase letters above upper 95% confidence limits indicate groups have different (non-matching letters) or not different (matching letters) means based on non-overlapping confidence intervals.

Published
2020
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50. The Legacy of Recurrent Introgression during the Radiation of Hares

Author

Ferreira, Mafalda S, Jones, Matthew R, Callahan, Colin M, Farelo, Liliana, Tolesa, Zelalem, Suchentrunk, Franz, Boursot, Pierre, Mills, L Scott, Alves, Paulo C, Good, Jeffrey M, Melo-Ferreira, José, Ferreira, Mafalda S, Jones, Matthew R, Callahan, Colin M, Farelo, Liliana, Tolesa, Zelalem, Suchentrunk, Franz, Boursot, Pierre, Mills, L Scott, Alves, Paulo C, Good, Jeffrey M, and Melo-Ferreira, José

Abstract

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1–4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation.

Published
2020
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