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3. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Author

Hoban, Sean, Bruford, Michael W., da Silva, Jessica M., Funk, W. Chris, Frankham, Richard, Gill, Michael J., Grueber, Catherine E., Heuertz, Myriam, Hunter, Margaret E., Kershaw, Francine, Lacy, Robert C., Lees, Caroline, Lopes-Fernandes, Margarida, MacDonald, Anna J., Mastretta-Yanes, Alicia, McGowan, Philip J. K., Meek, Mariah H., Mergeay, Joachim, Millette, Katie L., Mittan-Moreau, Cinnamon S., Navarro, Laetitia M., O’Brien, David, Ogden, Rob, Segelbacher, Gernot, Paz-Vinas, Ivan, Vernesi, Cristiano, and Laikre, Linda

Published
2023
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4. A population genetic analysis of the Critically Endangered Madagascar big-headed turtle, Erymnochelys madagascariensis across captive and wild populations

Author

White, Nina F. D., Mennell, Holly, Power, Georgia, Edwards, Dominic, Chrimes, Luke, Woolaver, Lance, Velosoa, Juliette, Randriamahita, Mozavelo, Richard, Rafeliarisoa, Tsilavo Hasina, Kuchling, Gerald, Lopez, Javier, Bekarany, Ernest, Charles, Namotoa, Young, Richard, Lewis, Richard, Bruford, Michael W., and Orozco-terWengel, Pablo

Published
2022
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5. Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation

Author

Scholz, Amber Hartman, Freitag, Jens, Lyal, Christopher H. C., Sara, Rodrigo, Cepeda, Martha Lucia, Cancio, Ibon, Sett, Scarlett, Hufton, Andrew Lee, Abebaw, Yemisrach, Bansal, Kailash, Benbouza, Halima, Boga, Hamadi Iddi, Brisse, Sylvain, Bruford, Michael W., Clissold, Hayley, Cochrane, Guy, Coddington, Jonathan A., Deletoille, Anne-Caroline, García-Cardona, Felipe, Hamer, Michelle, Hurtado-Ortiz, Raquel, Miano, Douglas W., Nicholson, David, Oliveira, Guilherme, Bravo, Carlos Ospina, Rohden, Fabian, Seberg, Ole, Segelbacher, Gernot, Shouche, Yogesh, Sierra, Alejandra, Karsch-Mizrachi, Ilene, da Silva, Jessica, Hautea, Desiree M., da Silva, Manuela, Suzuki, Mutsuaki, Tesfaye, Kassahun, Tiambo, Christian Keambou, Tolley, Krystal A., Varshney, Rajeev, Zambrano, María Mercedes, and Overmann, Jörg

Published
2022
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6. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints.

Author

Benjelloun, Badr, Leempoel, Kevin, Boyer, Frédéric, Stucki, Sylvie, Streeter, Ian, Orozco‐terWengel, Pablo, Alberto, Florian J., Servin, Bertrand, Biscarini, Filippo, Alberti, Adriana, Engelen, Stefan, Stella, Alessandra, Colli, Licia, Coissac, Eric, Bruford, Michael W., Ajmone‐Marsan, Paolo, Negrini, Riccardo, Clarke, Laura, Flicek, Paul, and Chikhi, Abdelkader

Subjects
DISTRIBUTION (Probability theory), GENETIC variation, RAINFALL, GENE frequency, SPRING, GOAT breeds
Abstract

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co‐distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco‐climatic gradients, and a differential role of climatic drivers on the two species, despite their co‐distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond. [ABSTRACT FROM AUTHOR]

Published
2024
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7. The positive impact of conservation action

Author

Langhammer, Penny F., primary, Bull, Joseph W., additional, Bicknell, Jake E., additional, Oakley, Joseph L., additional, Brown, Mary H., additional, Bruford, Michael W., additional, Butchart, Stuart H. M., additional, Carr, Jamie A., additional, Church, Don, additional, Cooney, Rosie, additional, Cutajar, Simone, additional, Foden, Wendy, additional, Foster, Matthew N., additional, Gascon, Claude, additional, Geldmann, Jonas, additional, Genovesi, Piero, additional, Hoffmann, Michael, additional, Howard-McCombe, Jo, additional, Lewis, Tiffany, additional, Macfarlane, Nicholas B. W., additional, Melvin, Zoe E., additional, Merizalde, Rossana Stoltz, additional, Morehouse, Meredith G., additional, Pagad, Shyama, additional, Polidoro, Beth, additional, Sechrest, Wes, additional, Segelbacher, Gernot, additional, Smith, Kevin G., additional, Steadman, Janna, additional, Strongin, Kyle, additional, Williams, Jake, additional, Woodley, Stephen, additional, and Brooks, Thomas M., additional

Published
2024
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8. Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

Author

Laikre, Linda, Hohenlohe, Paul A., Allendorf, Fred W., Bertola, Laura D., Breed, Martin F., Bruford, Michael W., Funk, W. Chris, Gajardo, Gonzalo, González-Rodríguez, Antonio, Grueber, Catherine E., Hedrick, Philip W., Heuertz, Myriam, Hunter, Margaret E., Johannesson, Kerstin, Liggins, Libby, MacDonald, Anna J., Mergeay, Joachim, Moharrek, Farideh, O’Brien, David, Ogden, Rob, Orozco-terWengel, Pablo, Palma-Silva, Clarisse, Pierson, Jennifer, Paz-Vinas, Ivan, Russo, Isa-Rita M., Ryman, Nils, Segelbacher, Gernot, Sjögren-Gulve, Per, Waits, Lisette P., Vernesi, Cristiano, and Hoban, Sean

Published
2021
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9. The Positive Impact of Conservation Action

Author

Langhammer, Penny, Bull, Joseph W., Bicknell, Jake E., Oakley, Joseph L., Brown, Mary H., Bruford, Michael W., Butchart, Stuart H.M., Carr, Jamie A., Church, Don, Cooney, Rosie, Cutajar, Simone, Foden, Wendy, Foster, Matthew N., Gascon, Claude, Geldmann, Jonas, Genovesi, Piero, Hoffmann, Michael, Howard-McCombe, Jo, Lewis, Tiffany, Macfarlane, Nicholas B.W., Melvin, Zoe E., Merizalde, Rossana G., Morehouse, Meredith G., Pagad, Shyama, Polidoro, Beth, Sechrest, Wes, Segelbacher, Gernot, Smith, Kevin G., Steadman, Janna, Strongin, Kyle, Williams, Jake, Woodley, Stephen, Brooks, Thomas M., Langhammer, Penny, Bull, Joseph W., Bicknell, Jake E., Oakley, Joseph L., Brown, Mary H., Bruford, Michael W., Butchart, Stuart H.M., Carr, Jamie A., Church, Don, Cooney, Rosie, Cutajar, Simone, Foden, Wendy, Foster, Matthew N., Gascon, Claude, Geldmann, Jonas, Genovesi, Piero, Hoffmann, Michael, Howard-McCombe, Jo, Lewis, Tiffany, Macfarlane, Nicholas B.W., Melvin, Zoe E., Merizalde, Rossana G., Morehouse, Meredith G., Pagad, Shyama, Polidoro, Beth, Sechrest, Wes, Segelbacher, Gernot, Smith, Kevin G., Steadman, Janna, Strongin, Kyle, Williams, Jake, Woodley, Stephen, and Brooks, Thomas M.

Abstract

Governments recently adopted new global targets to halt and reverse the loss of biodiversity. It is therefore crucial to understand the outcomes of conservation actions. We conducted a global meta-analysis of 186 studies (including 665 trials) that measured biodiversity over time and compared outcomes under conservation action with a suitable counterfactual of no action. We find that in two-thirds of cases, conservation either improved the state of biodiversity or at least slowed declines. Specifically, we find that interventions targeted at species and ecosystems, such as invasive species control, habitat loss reduction and restoration, protected areas, and sustainable management, are highly effective and have large effect sizes. This provides the strongest evidence to date that conservation actions are successful but require transformational scaling up to meet global targets.

Published
2024

10. A pragmatic approach for integrating molecular tools into biodiversity conservation

Author

Bertola, Laura D., Brüniche-Olsen, Anna, Kershaw, Francine, Russo, Isa Rita M., MacDonald, Anna J., Sunnucks, Paul, Bruford, Michael W., Cadena, Carlos Daniel, Ewart, Kyle M., de Bruyn, Mark, Eldridge, Mark D.B., Frankham, Richard, Guayasamin, Juan M., Grueber, Catherine E., Hoareau, Thierry B., Hoban, Sean, Hohenlohe, Paul A., Hunter, Margaret E., Kotze, Antoinette, Kuja, Josiah, Lacy, Robert C., Laikre, Linda, Lo, Nathan, Meek, Mariah H., Mergeay, Joachim, Mittan-Moreau, Cinnamon, Neaves, Linda E., O'Brien, David, Ochieng, Joel W., Ogden, Rob, Orozco-terWengel, Pablo, Páez-Vacas, Mónica, Pierson, Jennifer, Ralls, Katherine, Shaw, Robyn E., Sogbohossou, Etotépé A., Stow, Adam, Steeves, Tammy, Vernesi, Cristiano, Watsa, Mrinalini, Segelbacher, Gernot, Bertola, Laura D., Brüniche-Olsen, Anna, Kershaw, Francine, Russo, Isa Rita M., MacDonald, Anna J., Sunnucks, Paul, Bruford, Michael W., Cadena, Carlos Daniel, Ewart, Kyle M., de Bruyn, Mark, Eldridge, Mark D.B., Frankham, Richard, Guayasamin, Juan M., Grueber, Catherine E., Hoareau, Thierry B., Hoban, Sean, Hohenlohe, Paul A., Hunter, Margaret E., Kotze, Antoinette, Kuja, Josiah, Lacy, Robert C., Laikre, Linda, Lo, Nathan, Meek, Mariah H., Mergeay, Joachim, Mittan-Moreau, Cinnamon, Neaves, Linda E., O'Brien, David, Ochieng, Joel W., Ogden, Rob, Orozco-terWengel, Pablo, Páez-Vacas, Mónica, Pierson, Jennifer, Ralls, Katherine, Shaw, Robyn E., Sogbohossou, Etotépé A., Stow, Adam, Steeves, Tammy, Vernesi, Cristiano, Watsa, Mrinalini, and Segelbacher, Gernot

Abstract

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation., Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

Published
2024

11. Climate-driven flyway changes and memory-based long-distance migration

Author

Gu, Zhongru, Pan, Shengkai, Lin, Zhenzhen, Hu, Li, Dai, Xiaoyang, Chang, Jiang, Xue, Yuanchao, Su, Han, Long, Juan, Sun, Mengru, Ganusevich, Sergey, Sokolov, Vasiliy, Sokolov, Aleksandr, Pokrovsky, Ivan, Ji, Fen, and Bruford, Michael W.

Subjects
Migratory birds -- Environmental aspects -- Behavior, Climatic changes -- Environmental aspects, Peregrine falcon -- Environmental aspects -- Behavior, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic.sup.1, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds. The routes and lengths of migrations of Eurasian Arctic peregrine falcons have probably been shaped by climate change across the Last Glacial Maximum-Holocene transition and by selection for long-term memory acting on ADCY8, respectively., Author(s): Zhongru Gu [sup.1] [sup.2] [sup.3] , Shengkai Pan [sup.1] [sup.2] , Zhenzhen Lin [sup.1] [sup.2] , Li Hu [sup.1] [sup.2] [sup.3] , Xiaoyang Dai [sup.4] , Jiang Chang [sup.5] [...]

Published
2021
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12. Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

Author

Laikre, Linda, Hohenlohe, Paul A., Allendorf, Fred W., Bertola, Laura D., Breed, Martin F., Bruford, Michael W., Funk, W. Chris, Gajardo, Gonzalo, González-Rodríguez, Antonio, Grueber, Catherine E., Hedrick, Philip W., Heuertz, Myriam, Hunter, Margaret E., Johannesson, Kerstin, Liggins, Libby, MacDonald, Anna J., Mergeay, Joachim, Moharrek, Farideh, O’Brien, David, Ogden, Rob, Orozco-terWengel, Pablo, Palma-Silva, Clarisse, Pierson, Jennifer, Paz-Vinas, Ivan, Russo, Isa-Rita M., Ryman, Nils, Segelbacher, Gernot, Sjögren-Gulve, Per, Waits, Lisette P., Vernesi, Cristiano, and Hoban, Sean

Published
2021
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13. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints

Author

Benjelloun, Badr, primary, Leempoel, Kevin, additional, Boyer, Frédéric, additional, Stucki, Sylvie, additional, Streeter, Ian, additional, Orozco‐terWengel, Pablo, additional, Alberto, Florian J., additional, Servin, Bertrand, additional, Biscarini, Filippo, additional, Alberti, Adriana, additional, Engelen, Stefan, additional, Stella, Alessandra, additional, Colli, Licia, additional, Coissac, Eric, additional, Bruford, Michael W., additional, Ajmone‐Marsan, Paolo, additional, Negrini, Riccardo, additional, Clarke, Laura, additional, Flicek, Paul, additional, Chikhi, Abdelkader, additional, Joost, Stéphane, additional, Taberlet, Pierre, additional, and Pompanon, François, additional

Published
2023
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14. A pragmatic approach for integrating molecular tools into biodiversity conservation

Author

Bertola, Laura D., primary, Brüniche‐Olsen, Anna, additional, Kershaw, Francine, additional, Russo, Isa‐Rita M., additional, MacDonald, Anna J., additional, Sunnucks, Paul, additional, Bruford, Michael W., additional, Cadena, Carlos Daniel, additional, Ewart, Kyle M., additional, de Bruyn, Mark, additional, Eldridge, Mark D. B., additional, Frankham, Richard, additional, Guayasamin, Juan M., additional, Grueber, Catherine E., additional, Hoareau, Thierry B., additional, Hoban, Sean, additional, Hohenlohe, Paul A., additional, Hunter, Margaret E., additional, Kotze, Antoinette, additional, Kuja, Josiah, additional, Lacy, Robert C., additional, Laikre, Linda, additional, Lo, Nathan, additional, Meek, Mariah H., additional, Mergeay, Joachim, additional, Mittan‐Moreau, Cinnamon, additional, Neaves, Linda E., additional, O'Brien, David, additional, Ochieng, Joel W., additional, Ogden, Rob, additional, Orozco‐terWengel, Pablo, additional, Páez‐Vacas, Mónica, additional, Pierson, Jennifer, additional, Ralls, Katherine, additional, Shaw, Robyn E., additional, Sogbohossou, Etotépé A., additional, Stow, Adam, additional, Steeves, Tammy, additional, Vernesi, Cristiano, additional, Watsa, Mrinalini, additional, and Segelbacher, Gernot, additional

Published
2023
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15. High performance computation of landscape genomic models integrating local indices of spatial association

Author

Stucki, Sylvie, Orozco-terWengel, Pablo, Bruford, Michael W., Colli, Licia, Masembe, Charles, Negrini, Riccardo, Taberlet, Pierre, Joost, Stéphane, and Consortium, the NEXTGEN

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current challenges of the field mainly involve processing large numbers of models and disentangling selection from demography. Several methods address the latter, either by estimating a neutral model from population structure or by inferring simultaneously environmental and demographic effects. Here we present Sam$\beta$ada, an integrated approach to study signatures of local adaptation, providing rapid processing of whole genome data and enabling assessment of spatial association using molecular markers. Specifically, candidate loci to adaptation are identified by automatically assessing genome-environment associations. In complement, measuring the Local Indicators of Spatial Association (LISA) for these candidate loci allows to detect whether similar genotypes tend to gather in space, which constitutes a useful indication of the possible kinship relationship between individuals. In this paper, we also analyze SNP data from Ugandan cattle to detect signatures of local adaptation with Sam$\beta$ada, BayEnv, LFMM and an outlier method (FDIST approach in Arlequin) and compare their results. Sam$\beta$ada is an open source software for Windows, Linux and MacOS X available at \url{http://lasig.epfl.ch/sambada}, Comment: 1 figure in text, 1 figure in supplementary material The structure of the article was modified and some explanations were updated. The methods and results presented are the same as in the previous version

Published
2014
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19. Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858)

Author

D’Urban Jackson, Josephine, Bruford, Michael W., Székely, Tamás, DaCosta, Jeffrey M., Sorenson, Michael D., Russo, Isa-Rita M., Maher, Kathryn H., Cruz-López, Medardo, Galindo-Espinosa, Daniel, Palacios, Eduardo, De Sucre-Medrano, Atahualpa Eduardo, Cavitt, John, Pruner, Raya, Morales, Alcides L., Gonzalez, Oscar, Burke, Terry, and Küpper, Clemens

Published
2020
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21. Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M, Lee, Chul, Storz, Jay F, Antunes, Agostinho, Greenwold, Matthew J, Meredith, Robert W, Ödeen, Anders, Cui, Jie, Zhou, Qi, Xu, Luohao, Pan, Hailin, Wang, Zongji, Jin, Lijun, Zhang, Pei, Hu, Haofu, Yang, Wei, Hu, Jiang, Xiao, Jin, Yang, Zhikai, Liu, Yang, Xie, Qiaolin, Yu, Hao, Lian, Jinmin, Wen, Ping, Zhang, Fang, Li, Hui, Zeng, Yongli, Xiong, Zijun, Liu, Shiping, Zhou, Long, Huang, Zhiyong, An, Na, Wang, Jie, Zheng, Qiumei, Xiong, Yingqi, Wang, Guangbiao, Wang, Bo, Wang, Jingjing, Fan, Yu, da Fonseca, Rute R, Alfaro-Núñez, Alonzo, Schubert, Mikkel, Orlando, Ludovic, Mourier, Tobias, Howard, Jason T, Ganapathy, Ganeshkumar, Pfenning, Andreas, Whitney, Osceola, Rivas, Miriam V, Hara, Erina, Smith, Julia, Farré, Marta, Narayan, Jitendra, Slavov, Gancho, Romanov, Michael N, Borges, Rui, Machado, João Paulo, Khan, Imran, Springer, Mark S, Gatesy, John, Hoffmann, Federico G, Opazo, Juan C, Håstad, Olle, Sawyer, Roger H, Kim, Heebal, Kim, Kyu-Won, Kim, Hyeon Jeong, Cho, Seoae, Li, Ning, Huang, Yinhua, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Bertelsen, Mads F, Derryberry, Elizabeth, Warren, Wesley, Wilson, Richard K, Li, Shengbin, Ray, David A, Green, Richard E, O’Brien, Stephen J, Griffin, Darren, Johnson, Warren E, Haussler, David, Ryder, Oliver A, Willerslev, Eske, Graves, Gary R, Alström, Per, Fjeldså, Jon, Mindell, David P, Edwards, Scott V, Braun, Edward L, Rahbek, Carsten, Burt, David W, Houde, Peter, and Zhang, Yong

Subjects
Human Genome, Biotechnology, Genetics, Adaptation, Physiological, Animals, Biodiversity, Biological Evolution, Birds, Conserved Sequence, Diet, Evolution, Molecular, Female, Flight, Animal, Genes, Genetic Variation, Genome, Genomics, Male, Molecular Sequence Annotation, Phylogeny, Reproduction, Selection, Genetic, Sequence Analysis, DNA, Synteny, Vision, Ocular, Vocalization, Animal, Avian Genome Consortium, General Science & Technology
Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Published
2014

22. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author

Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, Mindell, David P, and Cracraft, Joel

Subjects
Human Genome, Genetics, Animals, Avian Proteins, Base Sequence, Biological Evolution, Birds, DNA Transposable Elements, Genes, Genetic Speciation, Genome, INDEL Mutation, Introns, Phylogeny, Sequence Analysis, DNA, General Science & Technology
Abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Published
2014

23. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros

Author

Sánchez-Barreiro, Fátima, primary, De Cahsan, Binia, additional, Westbury, Michael V, additional, Sun, Xin, additional, Margaryan, Ashot, additional, Fontsere, Claudia, additional, Bruford, Michael W, additional, Russo, Isa-Rita M, additional, Kalthoff, Daniela C, additional, Sicheritz-Pontén, Thomas, additional, Petersen, Bent, additional, Dalén, Love, additional, Zhang, Guojie, additional, Marquès-Bonet, Tomás, additional, Gilbert, M Thomas P, additional, and Moodley, Yoshan, additional

Published
2023
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33. Polygamy slows down population divergence in shorebirds

Author

Jackson, Josephine D’Urban, dos Remedios, Natalie, Maher, Kathryn H., Zefania, Sama, Haig, Susan, Oyler-McCance, Sara, Blomqvist, Donald, Burke, Terry, Bruford, Michael W., Székely, Tamás, and Küpper, Clemens

Published
2017

34. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Author

Li, Xin, Yang, Ji, Shen, Min, Xie, Xing-Long, Liu, Guang-Jian, Xu, Ya-Xi, Lv, Feng-Hua, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Zhou, Ping, Wan, Peng-Cheng, Zhang, Yun-Sheng, Gao, Lei, Yang, Jing-Quan, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Deng, Juan, Xu, Song-Song, Salehian-Dehkordi, Hosein, Hehua, Eer, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Štěpánek, Ondřej, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Lenstra, Johannes A., Kantanen, Juha, Coltman, David W., Kijas, James W., Bruford, Michael W., Periasamy, Kathiravan, Wang, Xin-Hua, and Li, Meng-Hua

Published
2020
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46. Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

Author

Howard-McCombe, Jo, Jamieson, Alexandra, Carmagnini, Alberto, Russo, Isa-Rita M., Ghazali, Muhammad, Campbell, Ruairidh, Driscoll, Carlos, Murphy, William J., Nowak, Carsten, O’Connor, Terry, Tomsett, Louise, Lyons, Leslie A., Muñoz-Fuentes, Violeta, Bruford, Michael W., Kitchener, Andrew C., Larson, Greger, Frantz, Laurent, Senn, Helen, Lawson, Daniel J., and Beaumont, Mark A.

Published
2023
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48. Behavior Predicts Genetic Structure in a Wild Primate Group

Author

Altmann, Jeanne, Alberts, Susan C., Haines, Susan A., Dubach, Jean, Muruthi, Philip, Coote, Trevor, Geffen, Eli, Cheesman, David J., Mututua, Raphael S., Saiyalel, Serah N., Wayne, Robert K., Lacy, Robert C., and Bruford, Michael W.

Published
1996

49. Historic Sampling of a Vanishing Beast:Population Structure and Diversity in the Black Rhinoceros

Author

Sánchez-Barreiro, Fátima, De Cahsan, Binia, Westbury, Michael V., Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, Michael W., Russo, Isa-Rita M., Kalthoff, Daniela C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, Love, Zhang, Guojie, Marquès-Bonet, Tomás, Gilbert, M. Thomas P., Moodley, Yoshan, Sánchez-Barreiro, Fátima, De Cahsan, Binia, Westbury, Michael V., Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, Michael W., Russo, Isa-Rita M., Kalthoff, Daniela C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, Love, Zhang, Guojie, Marquès-Bonet, Tomás, Gilbert, M. Thomas P., and Moodley, Yoshan

Abstract

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

Published
2023

50. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros

Author

EMBO, European Commission, Knut and Alice Wallenberg Foundation, European Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), National Research Foundation (South Africa), Natural History Museum (UK), Museum of Natural History (Germany), Hungarian Natural History Museum, Sánchez-Barreiro, Fátima, Cahsan, Binia de, Westbury, Michael V., Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, Michael W., Russo, Isa-Rita M., Kalthoff, Daniela C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, Love, Zhang, Guojie, Marqués-Bonet, Tomàs, Gilbert, M. Thomas P., Moodley, Yoshan, EMBO, European Commission, Knut and Alice Wallenberg Foundation, European Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), National Research Foundation (South Africa), Natural History Museum (UK), Museum of Natural History (Germany), Hungarian Natural History Museum, Sánchez-Barreiro, Fátima, Cahsan, Binia de, Westbury, Michael V., Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, Michael W., Russo, Isa-Rita M., Kalthoff, Daniela C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, Love, Zhang, Guojie, Marqués-Bonet, Tomàs, Gilbert, M. Thomas P., and Moodley, Yoshan

Abstract

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

Published
2023

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