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1. 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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2. 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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3. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske

Subjects
Asia, DNA, Ancient, Europe, Gene Pool, Genome, Human, Haplotypes, History, 15th Century, History, Ancient, History, Medieval, Human Migration, Humans, Indians, North American, Male, Siberia, General Science & Technology
Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Published
2019

4. Recurrent selection shapes the genomic landscape of differentiation between a pair of host‐specialized haplodiploids that diverged with gene flow.

Author

Glover, Ashleigh N., Sousa, Vitor C., Ridenbaugh, Ryan D., Sim, Sheina B., Geib, Scott M., and Linnen, Catherine R.

Subjects
*SEX chromosomes, *GENETIC variation, *HAPLODIPLOIDY, *SAWFLIES, *GENETICS, *GENE flow
Abstract

Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non‐exclusive processes in shaping genome‐wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole‐genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister‐species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome‐wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage‐specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome‐wide patterns of genetic variation. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Conservation Challenges Imposed by Evolutionary History and Habitat Suitability Shifts of Endangered Freshwater Mussels under a Global Climate Change Scenario

Author

Reis, Joaquim, primary, Perea, Silvia, additional, Gama, Mafalda, additional, Mendes, Sofia L., additional, Sousa, Vitor C., additional, Lima, Cristina, additional, Banha, Filipe, additional, Gil, Maria, additional, Alvarez, Maria Garcia, additional, Anastácio, Pedro, additional, Sousa Santos, Carla, additional, and Araujo, Rafael, additional

Published
2024
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7. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Author

Sikora, Martin, Seguin-Orlando, Andaine, Sousa, Vitor C, Albrechtsen, Anders, Korneliussen, Thorfinn, Ko, Amy, Rasmussen, Simon, Dupanloup, Isabelle, Nigst, Philip R, Bosch, Marjolein D, Renaud, Gabriel, Allentoft, Morten E, Margaryan, Ashot, Vasilyev, Sergey V, Veselovskaya, Elizaveta V, Borutskaya, Svetlana B, Deviese, Thibaut, Comeskey, Dan, Higham, Tom, Manica, Andrea, Foley, Robert, Meltzer, David J, Nielsen, Rasmus, Excoffier, Laurent, Mirazon Lahr, Marta, Orlando, Ludovic, and Willerslev, Eske

Subjects
Biological Sciences, Anthropology, Genetics, Human Society, DNA, Ancient, Genome, Human, History, Ancient, Humans, Population Density, Reproductive Behavior, Russia, Social Behavior, General Science & Technology
Abstract

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Published
2017

8. Conservation Challenges Imposed by Evolutionary History and Habitat Suitability Shifts of Endangered Freshwater Mussels under a Global Climate Change Scenario

Author

Fundação para a Ciência e a Tecnologia (Portugal), Reis, Joaquim, Perea, Silvia, Gama, Mafalda, Mendes, Sofia L., Sousa, Vitor C., Lima, Cristina, Banha, Filipe, Gil, Maria, Alvarez, Maria Garcia, Anastácio, Pedro, Sousa Santos, Carla, Araujo, Rafael, Fundação para a Ciência e a Tecnologia (Portugal), Reis, Joaquim, Perea, Silvia, Gama, Mafalda, Mendes, Sofia L., Sousa, Vitor C., Lima, Cristina, Banha, Filipe, Gil, Maria, Alvarez, Maria Garcia, Anastácio, Pedro, Sousa Santos, Carla, and Araujo, Rafael

Abstract

Climate change and associated shifts in temperature and precipitation patterns have become an increasing concern as drivers of ongoing biodiversity loss. The Mediterranean region is particularly vulnerable, being both a biodiversity hotspot and a region very prone to desertification. Freshwater mussels are amongst the most threatened invertebrate taxa worldwide. Unio tumidiformis is an endemic and endangered species restricted to the southern Iberian Peninsula, living in temporary Mediterranean-type streams. Freshwater mussels need a fish host for successful larval transformation, meaning U. tumidiformis must belong to the genus Squalius. The main objective of this study was to evaluate the vulnerability of U. tumidiformis to climate change, by studying its population genetics and evolutionary history, its current and future habitat suitability, and that of its hosts. Genetic population structure and diversity were assessed using Single-Nucleotide Polymorphisms through Genotyping by Sequencing and used to infer species evolutionary history. The species potential distribution was modeled using an ensemble forecasting approach, and future shifts in habitat suitability were assessed with the projected climate data layers from Worldclim. Most populations showed extreme genetic differentiation (Fst up to 0.745), even from close neighboring ones. Upper Guadiana populations were more diverse and less differentiated. We hypothesize that U. tumidiformis originated in Upper Guadiana and followed the same colonization routes as their hosts with numerous founder effects and bottlenecks. Our results also predicted a reduction of 99% of climatically suitable areas for U. tumidiformis in the Iberian Peninsula until 2040. For the fish hosts, a maximum 42% reduction in suitable areas was estimated throughout the century, with remaining adequate habitats in the north. Our results suggest that difficult conservation options are necessary, prioritizing the preservation of populations

Published
2024

9. A genomic history of Aboriginal Australia

Author

Malaspinas, Anna-Sapfo, Westaway, Michael C, Muller, Craig, Sousa, Vitor C, Lao, Oscar, Alves, Isabel, Bergström, Anders, Athanasiadis, Georgios, Cheng, Jade Y, Crawford, Jacob E, Heupink, Tim H, Macholdt, Enrico, Peischl, Stephan, Rasmussen, Simon, Schiffels, Stephan, Subramanian, Sankar, Wright, Joanne L, Albrechtsen, Anders, Barbieri, Chiara, Dupanloup, Isabelle, Eriksson, Anders, Margaryan, Ashot, Moltke, Ida, Pugach, Irina, Korneliussen, Thorfinn S, Levkivskyi, Ivan P, Moreno-Mayar, J Víctor, Ni, Shengyu, Racimo, Fernando, Sikora, Martin, Xue, Yali, Aghakhanian, Farhang A, Brucato, Nicolas, Brunak, Søren, Campos, Paula F, Clark, Warren, Ellingvåg, Sturla, Fourmile, Gudjugudju, Gerbault, Pascale, Injie, Darren, Koki, George, Leavesley, Matthew, Logan, Betty, Lynch, Aubrey, Matisoo-Smith, Elizabeth A, McAllister, Peter J, Mentzer, Alexander J, Metspalu, Mait, Migliano, Andrea B, Murgha, Les, Phipps, Maude E, Pomat, William, Reynolds, Doc, Ricaut, Francois-Xavier, Siba, Peter, Thomas, Mark G, Wales, Thomas, Wall, Colleen Ma’run, Oppenheimer, Stephen J, Tyler-Smith, Chris, Durbin, Richard, Dortch, Joe, Manica, Andrea, Schierup, Mikkel H, Foley, Robert A, Lahr, Marta Mirazón, Bowern, Claire, Wall, Jeffrey D, Mailund, Thomas, Stoneking, Mark, Nielsen, Rasmus, Sandhu, Manjinder S, Excoffier, Laurent, Lambert, David M, and Willerslev, Eske

Subjects
Africa, Australia, Datasets as Topic, Desert Climate, Gene Flow, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Language, Native Hawaiian or Other Pacific Islander, New Guinea, Phylogeny, Population Dynamics, Racial Groups, Tasmania, General Science & Technology
Abstract

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

Published
2016

12. 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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16. Chimpanzee genomic diversity reveals ancient admixture with bonobos

Author

de Manuel, Marc, Kuhlwilm, Martin, Frandsen, Peter, Sousa, Vitor C., Desai, Tariq, Prado-Martinez, Javier, Hernandez-Rodriguez, Jessica, Dupanloup, Isabelle, Lao, Oscar, Hallast, Pille, Schmidt, Joshua M., Heredia-Genestar, José María, Benazzo, Andrea, Barbujani, Guido, Peter, Benjamin M., Kuderna, Lukas F. K., Casals, Ferran, Angedakin, Samuel, Arandjelovic, Mimi, Boesch, Christophe, Kühl, Hjalmar, Vigilant, Linda, Langergraber, Kevin, Novembre, John, Gut, Marta, Gut, Ivo, Navarro, Arcadi, Carlsen, Frauds, Andres, Aida M., Siegismund, Hans. R., Scally, Aylwyn, Excoffier, Laurent, Tyler-Smith, Chris, Castellano, Sergi, Xue, Yali, Hvilsom, Christina, and Marques-Bonet, Tomas

Published
2016

18. Applying genomic approaches to delineate conservation strategies using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula as a model

Author

Perea, S., Mendes, Sofia L., Sousa-Santos, C., Ondina, P., Amaro, R., Castro, J., San-Miguel, E., Lima, C. S., Garcia, M., Velasquez, V., Garcia-Roves, P., Fernández, D., Araujo, R., Sousa, Vitor C, Reis, J., Fundação para a Ciência e a Tecnologia (Portugal), ARNET associated laboratory, and Repositório da Universidade de Lisboa

Subjects
Multidisciplinary, Seafood, Fresh water, Trout, Genetic Variation, Animals, Fresh Water, Genetic variation, Genomics, Bivalvia
Abstract

Effective conservation actions to counteract the current decline of populations and species require a deep knowledge on their genetic structure. We used Single Nucleotide Polymorphisms (SNPs) to infer the population structure of the highly threatened freshwater pearl mussel Margaritifera margaritifera in the Iberian Peninsula. A total of 130 individuals were collected from 26 locations belonging to 16 basins. We obtained 31,692 SNPs through Genotyping by Sequencing (GBS) and used this dataset to infer population structure. Genetic diversity given as observed heterozygosity was low. Pairwise FST comparisons revealed low levels of genetic differentiation among geographically close populations. Up to 3 major genetic lineages were determined: Atlantic, Cantabrian and Douro. This structure suggests a close co-evolutionary process with brown trout (Salmo trutta), the primordial fish host of this mussel in the studied area. Some sub-basins showed some genetic structuring, whereas in others no intrapopulation differentiation was found. Our results confirm that genetic conservation units do not match individual basins, and that knowledge about the genetic structure is necessary before planning recovery plans that may involve relocation or restocking. The same reasoning should be applied to strictly freshwater species that are sessile or have restricted dispersal abilities and are currently imperiled worldwide., This work was supported by national funds of the Portuguese Foundation for Science and Technology (FCT) through the project MUSSELFLOW (contract PTDC/BIA- EVL/29199/2017) and under the strategic project LA/P/0069/2020 granted to the Associate Laboratory ARNET; and the grant awarded to C.S. Lima (MARE-ISPA/BI/004/2015).

Published
2022

26. The genomic history of the Aegean palatial civilizations

Author

Clemente, Florian, Unterlaender, Martina, Dolgova, Olga, Amorim, Carlos Eduardo G., Coroado-Santos, Francisco, Neuenschwander, Samuel, Ganiatsou, Elissavet, Davalos, Diana I. Cruz, Anchieri, Lucas, Michaud, Frederic, Winkelbach, Laura, Bloecher, Jens, Cardenas, Yami Ommar Arizmendi, da Mota, Barbara Sousa, Kalliga, Eleni, Souleles, Angelos, Kontopoulos, Ioannis, Karamitrou-Mentessidi, Georgia, Philaniotou, Olga, Sampson, Adamantios, Theodorou, Dimitra, Tsipopoulou, Metaxia, Akamatis, Ioannis, Halstead, Paul, Kotsakis, Kostas, Urem-Kotsou, Dushka, Panagiotopoulos, Diamantis, Ziota, Christina, Triantaphyllou, Sevasti, Delaneau, Olivier, Jensen, Jeffrey D., Victor Moreno-Mayar, J., Burger, Joachim, Sousa, Vitor C., Lao, Oscar, Malaspinas, Anna-Sapfo, Papageorgopoulou, Christina, Clemente, Florian, Unterlaender, Martina, Dolgova, Olga, Amorim, Carlos Eduardo G., Coroado-Santos, Francisco, Neuenschwander, Samuel, Ganiatsou, Elissavet, Davalos, Diana I. Cruz, Anchieri, Lucas, Michaud, Frederic, Winkelbach, Laura, Bloecher, Jens, Cardenas, Yami Ommar Arizmendi, da Mota, Barbara Sousa, Kalliga, Eleni, Souleles, Angelos, Kontopoulos, Ioannis, Karamitrou-Mentessidi, Georgia, Philaniotou, Olga, Sampson, Adamantios, Theodorou, Dimitra, Tsipopoulou, Metaxia, Akamatis, Ioannis, Halstead, Paul, Kotsakis, Kostas, Urem-Kotsou, Dushka, Panagiotopoulos, Diamantis, Ziota, Christina, Triantaphyllou, Sevasti, Delaneau, Olivier, Jensen, Jeffrey D., Victor Moreno-Mayar, J., Burger, Joachim, Sousa, Vitor C., Lao, Oscar, Malaspinas, Anna-Sapfo, and Papageorgopoulou, Christina

Abstract

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic- EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing similar to 50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.

Published
2021

28. The genomic history of the Aegean palatial civilizations

Author

Clemente, Florian, primary, Unterländer, Martina, additional, Dolgova, Olga, additional, Amorim, Carlos Eduardo G., additional, Coroado-Santos, Francisco, additional, Neuenschwander, Samuel, additional, Ganiatsou, Elissavet, additional, Cruz Dávalos, Diana I., additional, Anchieri, Lucas, additional, Michaud, Frédéric, additional, Winkelbach, Laura, additional, Blöcher, Jens, additional, Arizmendi Cárdenas, Yami Ommar, additional, Sousa da Mota, Bárbara, additional, Kalliga, Eleni, additional, Souleles, Angelos, additional, Kontopoulos, Ioannis, additional, Karamitrou-Mentessidi, Georgia, additional, Philaniotou, Olga, additional, Sampson, Adamantios, additional, Theodorou, Dimitra, additional, Tsipopoulou, Metaxia, additional, Akamatis, Ioannis, additional, Halstead, Paul, additional, Kotsakis, Kostas, additional, Urem-Kotsou, Dushka, additional, Panagiotopoulos, Diamantis, additional, Ziota, Christina, additional, Triantaphyllou, Sevasti, additional, Delaneau, Olivier, additional, Jensen, Jeffrey D., additional, Moreno-Mayar, J. Víctor, additional, Burger, Joachim, additional, Sousa, Vitor C., additional, Lao, Oscar, additional, Malaspinas, Anna-Sapfo, additional, and Papageorgopoulou, Christina, additional

Published
2021
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35. Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization

Author

Meier, Joana I, Sousa, Vitor C, Marques, David A, Selz, Oliver M, Wagner, Catherine E, Excoffier, Laurent, Seehausen, Ole, Marques, David A [0000-0003-4590-4575], Selz, Oliver M [0000-0002-2210-5909], and Apollo - University of Cambridge Repository

Subjects
Gene Flow, Sympatry, Genetics, Population, Models, Genetic, hybrid speciation, Genetic Speciation, demographic modelling, ecological speciation, Animals, Hybridization, Genetic, Cichlids, adaptive radiation, cichlid fish
Abstract

Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.

Published
2019
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36. Adaptation and convergence in genes of the circadian system in Iberian Squalius freshwater species

Author

Moreno, João M, Sousa, Vitor C, Jesus, Tiago F, and Coelho, Maria M

Abstract

The circadian clock is a biological timing system that improves the inherent ability of organisms to deal with environmental fluctuations. It is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, have an increased dependence on the environmental temperature and thus are good models to study the integration of temperature within the circadian system. Here, we studied four species of freshwater fish of Squalius genus, distributed across a latitudinal gradient in Portugal with variable conditions of light and temperature. We identified and characterised the expected sixteen genes belonging to four main gene families (Cryptochromes, Period, CLOCK and BMAL) involved in the circadian system. We conducted phylogenetic analysis and tested these genes for the presence of signatures of selection based on dN/dS that revealed the presence of mutations under positive selection in nine genes. Furthermore, we analysed functional features of the proteins and found that these mutations alter protein isoelectric point and aliphatic index. Additionally, in 50% of the genes we found a pattern of convergence uncovered by the phylogenetic clustering of S. aradensis and S. pyrenaicus from Almargem, which inhabit basins with similar environmental conditions. Although this clustering can be explained by incomplete lineage sorting, evidence of positive selection in one gene in the two species and similar functional features in seven proteins are consistent with convergence at protein level. Our results highlight the importance of integrating sequence-based functional protein characterisation with dN/dS-based methods when studying the molecular adaptation of species.

Published
2019
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37. Ancient admixture from an extinct ape lineage into bonobos

Author

German Research Foundation, Fundação para a Ciência e a Tecnologia (Portugal), Swiss National Science Foundation, European Commission, Fundación la Caixa, Generalitat de Catalunya, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuhlwilm, Martin, Han, Sojung, Sousa, Vitor C., Excoffier, Laurent, Marqués-Bonet, Tomàs, German Research Foundation, Fundação para a Ciência e a Tecnologia (Portugal), Swiss National Science Foundation, European Commission, Fundación la Caixa, Generalitat de Catalunya, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuhlwilm, Martin, Han, Sojung, Sousa, Vitor C., Excoffier, Laurent, and Marqués-Bonet, Tomàs

Abstract

Admixture is a recurrent phenomenon in humans and other great ape populations. Genetic information from extinct hominins allows us to study historical interactions with modern humans and discover adaptive functions of gene flow. Here, we investigate whole genomes from bonobo and chimpanzee populations for signatures of gene flow from unknown archaic populations, finding evidence for an ancient admixture event between bonobos and a divergent lineage. This result reveals a complex population history in our closest living relatives, probably several hundred thousand years ago. We reconstruct up to 4.8% of the genome of this ‘ghost’ ape, which represents genomic data of an extinct great ape population. Genes contained in archaic fragments might confer functional consequences for the immunity, behaviour and physiology of bonobos. Finally, comparing the landscapes of introgressed regions in humans and bonobos, we find that a recurrent depletion of introgression is rare, suggesting that genomic incompatibilities arose seldom in these lineages.

Published
2019

41. Genomic signatures of introgression between commercial and native bumblebees,Bombus terrestris, in western Iberian Peninsula—Implications for conservation and trade regulation

Author

Seabra, Sofia G., primary, Silva, Sara E., additional, Nunes, Vera L., additional, Sousa, Vitor C., additional, Martins, Joana, additional, Marabuto, Eduardo, additional, Rodrigues, Ana S. B., additional, Pina‐Martins, Francisco, additional, Laurentino, Telma G., additional, Rebelo, Maria Teresa, additional, Figueiredo, Elisabete, additional, and Paulo, Octávio S., additional

Published
2019
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42. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, primary, Pitulko, Vladimir V., additional, Sousa, Vitor C., additional, Allentoft, Morten E., additional, Vinner, Lasse, additional, Rasmussen, Simon, additional, Margaryan, Ashot, additional, de Barros Damgaard, Peter, additional, de la Fuente Castro, Constanza, additional, Renaud, Gabriel, additional, Yang, Melinda, additional, Fu, Qiaomei, additional, Dupanloup, Isabelle, additional, Giampoudakis, Konstantinos, additional, Bravo Nogues, David, additional, Rahbek, Carsten, additional, Kroonen, Guus, additional, Peyrot, Michäel, additional, McColl, Hugh, additional, Vasilyev, Sergey V., additional, Veselovskaya, Elizaveta, additional, Gerasimova, Margarita, additional, Pavlova, Elena Y., additional, Chasnyk, Vyacheslav G., additional, Nikolskiy, Pavel A., additional, Grebenyuk, Pavel S., additional, Fedorchenko, Alexander Yu., additional, Lebedintsev, Alexander I., additional, Slobodin, Sergey B., additional, Malyarchuk, Boris A., additional, Martiniano, Rui, additional, Meldgaard, Morten, additional, Arppe, Laura, additional, Palo, Jukka U., additional, Sundell, Tarja, additional, Mannermaa, Kristiina, additional, Putkonen, Mikko, additional, Alexandersen, Verner, additional, Primeau, Charlotte, additional, Mahli, Ripan, additional, Sjögren, Karl-Göran, additional, Kristiansen, Kristian, additional, Wessman, Anna, additional, Sajantila, Antti, additional, Lahr, Marta Mirazon, additional, Durbin, Richard, additional, Nielsen, Rasmus, additional, Meltzer, David J., additional, Excoffier, Laurent, additional, and Willerslev, Eske, additional

Published
2018
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48. Rapid host-plant adaptation in the herbivorous spider mite Tetranychus urticaeoccurs at low cost

Author

Sousa, Vitor C, Zélé, Flore, Rodrigues, Leonor R, Godinho, Diogo P, Charlery de la Masselière, Maud, and Magalhães, Sara

Abstract

•Spider-mites represent an excellent system to study host-plant adaptation.•When accounting for isolation-by-distance, host races are rare in Tetranychus urticae.•Experimental evolution studies reveal rapid host-plant adaptation at low cost.•Integrating genomics and phenotypic data holds potential to unravel host adaptation.

Published
2019
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49. Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in western Iberian Peninsula—Implications for conservation and trade regulation.

Author

Seabra, Sofia G., Silva, Sara E., Nunes, Vera L., Sousa, Vitor C., Martins, Joana, Marabuto, Eduardo, Rodrigues, Ana S. B., Pina‐Martins, Francisco, Laurentino, Telma G., Rebelo, Maria Teresa, Figueiredo, Elisabete, and Paulo, Octávio S.

Subjects
BOMBUS terrestris, CYTOCHROME oxidase, TRADE regulation, BUMBLEBEES, INTRODUCED species, GENETIC markers
Abstract

Human‐mediated introductions of species may have profound impacts on native ecosystems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pollination with known negative impacts on native pollinators. Given the likely allochthonous origin of commercial bumblebees used in Portugal (subspecies Bombus terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgression with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mitochondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome‐wide restriction‐site‐associated DNA markers (RAD‐seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the greenhouses where the commercial hives are used. In the RAD‐seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore, we detected candidate hybrids in the wild, as well as putatively escaped commercial bumblebees, some of which being potentially fertile males. Although we cannot assess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibility of using local subspecies B. t. lusitanicus, preferably with local production, should be evaluated. [ABSTRACT FROM AUTHOR]

Published
2019
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50. Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

Author

Foote, Andrew D., Vijay, Nagarjun, Avila-Arcos, Maria C., Baird, Robin W., Durban, John W., Fumagalli, Matteo, Gibbs, Richard A., Hanson, M. Bradley, Korneliussen, Thorfinn S., Martin, Michael D., Robertson, Kelly M., Sousa, Vitor C., Vieira, Filipe G., Vinar, Tomas, Wade, Paul, Worley, Kim C., Excoffier, Laurent, Morin, Phillip A., Gilbert, M. Thomas P., Wolf, Jochen B. W., Foote, Andrew D., Vijay, Nagarjun, Avila-Arcos, Maria C., Baird, Robin W., Durban, John W., Fumagalli, Matteo, Gibbs, Richard A., Hanson, M. Bradley, Korneliussen, Thorfinn S., Martin, Michael D., Robertson, Kelly M., Sousa, Vitor C., Vieira, Filipe G., Vinar, Tomas, Wade, Paul, Worley, Kim C., Excoffier, Laurent, Morin, Phillip A., Gilbert, M. Thomas P., and Wolf, Jochen B. W.

Abstract

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

Published
2016
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