Search

Your search keyword '"Ryder, Oliver"' showing total 1,098 results
Start Over Author "Ryder, Oliver"
1,098 results on '"Ryder, Oliver"'

1. Advancing stem cell technologies for conservation of wildlife biodiversity.

Author

Hutchinson, Ashlee M, Appeltant, Ruth, Burdon, Tom, Bao, Qiuye, Bargaje, Rhishikesh, Bodnar, Andrea, Chambers, Stuart, Comizzoli, Pierre, Cook, Laura, Endo, Yoshinori, Harman, Bob, Hayashi, Katsuhiko, Hildebrandt, Thomas, Korody, Marisa L, Lakshmipathy, Uma, Loring, Jeanne F, Munger, Clara, Ng, Alex HM, Novak, Ben, Onuma, Manabu, Ord, Sara, Paris, Monique, Pask, Andrew J, Pelegri, Francisco, Pera, Martin, Phelan, Ryan, Rosental, Benyamin, Ryder, Oliver A, Sukparangsi, Woranop, Sullivan, Gareth, Tay, Nicole Liling, Traylor-Knowles, Nikki, Walker, Shawn, Weberling, Antonia, Whitworth, Deanne J, Williams, Suzannah A, Wojtusik, Jessye, Wu, Jun, Ying, Qi-Long, Zwaka, Thomas P, and Kohler, Timo N

Subjects
In vitro gametogenesis, Biodiversity, Conservation, Disease modelling, IPSC, Stem cells, Animals, Conservation of Natural Resources, Animals, Wild, Stem Cells, Humans, Biological Sciences, Medical and Health Sciences, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Published
2024

3. The complete sequence and comparative analysis of ape sex chromosomes

Author

Makova, Kateryna D., Pickett, Brandon D., Harris, Robert S., Hartley, Gabrielle A., Cechova, Monika, Pal, Karol, Nurk, Sergey, Yoo, DongAhn, Li, Qiuhui, Hebbar, Prajna, McGrath, Barbara C., Antonacci, Francesca, Aubel, Margaux, Biddanda, Arjun, Borchers, Matthew, Bornberg-Bauer, Erich, Bouffard, Gerard G., Brooks, Shelise Y., Carbone, Lucia, Carrel, Laura, Carroll, Andrew, Chang, Pi-Chuan, Chin, Chen-Shan, Cook, Daniel E., Craig, Sarah J. C., de Gennaro, Luciana, Diekhans, Mark, Dutra, Amalia, Garcia, Gage H., Grady, Patrick G. S., Green, Richard E., Haddad, Diana, Hallast, Pille, Harvey, William T., Hickey, Glenn, Hillis, David A., Hoyt, Savannah J., Jeong, Hyeonsoo, Kamali, Kaivan, Pond, Sergei L. Kosakovsky, LaPolice, Troy M., Lee, Charles, Lewis, Alexandra P., Loh, Yong-Hwee E., Masterson, Patrick, McGarvey, Kelly M., McCoy, Rajiv C., Medvedev, Paul, Miga, Karen H., Munson, Katherine M., Pak, Evgenia, Paten, Benedict, Pinto, Brendan J., Potapova, Tamara, Rhie, Arang, Rocha, Joana L., Ryabov, Fedor, Ryder, Oliver A., Sacco, Samuel, Shafin, Kishwar, Shepelev, Valery A., Slon, Viviane, Solar, Steven J., Storer, Jessica M., Sudmant, Peter H., Sweetalana, Sweeten, Alex, Tassia, Michael G., Thibaud-Nissen, Françoise, Ventura, Mario, Wilson, Melissa A., Young, Alice C., Zeng, Huiqing, Zhang, Xinru, Szpiech, Zachary A., Huber, Christian D., Gerton, Jennifer L., Yi, Soojin V., Schatz, Michael C., Alexandrov, Ivan A., Koren, Sergey, O’Neill, Rachel J., Eichler, Evan E., and Phillippy, Adam M.

Published
2024
Full Text
View/download PDF

4. A genomic timescale for placental mammal evolution

Author

Foley, Nicole M, Mason, Victor C, Harris, Andrew J, Bredemeyer, Kevin R, Damas, Joana, Lewin, Harris A, Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Springer, Mark S, Murphy, William J, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Fan, Kaili, Fanter, Cornelia, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, and Sundström, Elisabeth

Subjects
Genetics, Human Genome, Biotechnology, Animals, Female, Biological Evolution, Eutheria, Evolution, Molecular, Fossils, Genomics, Phylogeny, Genetic Variation, Time Factors, Zoonomia Consortium‡, General Science & Technology
Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Published
2023

5. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs

Author

Moon, Katherine L, Huson, Heather J, Morrill, Kathleen, Wang, Ming-Shan, Li, Xue, Srikanth, Krishnamoorthy, Lindblad-Toh, Kerstin, Svenson, Gavin J, Karlsson, Elinor K, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, Sundström, Elisabeth, Supple, Megan A, and Swofford, Ross

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Animals, Dogs, Male, Genome, Genomics, Genotype, Phenotype, Wolves, Biodiversity, Genetic Variation, Zoonomia Consortium, General Science & Technology
Abstract

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

Published
2023

6. The contribution of historical processes to contemporary extinction risk in placental mammals

Author

Wilder, Aryn P, Supple, Megan A, Subramanian, Ayshwarya, Mudide, Anish, Swofford, Ross, Serres-Armero, Aitor, Steiner, Cynthia, Koepfli, Klaus-Peter, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Marques-Bonet, Tomas, Munoz Fuentes, Violeta, Foley, Kathleen, Meyer, Wynn K, Ryder, Oliver A, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, and Srinivasan, Chaitanya

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Behavioral and Social Science, Human Genome, Basic Behavioral and Social Science, Life on Land, Animals, Female, Pregnancy, Eutheria, Extinction, Biological, Genetic Variation, Genome, Population Density, Risk, Zoonomia Consortium‡, General Science & Technology
Abstract

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Published
2023

7. The functional and evolutionary impacts of human-specific deletions in conserved elements

Author

Xue, James R, Mackay-Smith, Ava, Mouri, Kousuke, Garcia, Meilin Fernandez, Dong, Michael X, Akers, Jared F, Noble, Mark, Li, Xue, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Noonan, James P, Capellini, Terence D, Brennand, Kristen J, Tewhey, Ryan, Sabeti, Pardis C, Reilly, Steven K, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, and Steiner, Cynthia

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Neurological, Humans, Conserved Sequence, Evolution, Molecular, Genome, Genomics, RNA-Binding Proteins, Sequence Deletion, Brain, Gene Expression Regulation, Developmental, Zoonomia Consortium†, General Science & Technology
Abstract

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Published
2023

8. Integrating gene annotation with orthology inference at scale

Author

Kirilenko, Bogdan M, Munegowda, Chetan, Osipova, Ekaterina, Jebb, David, Sharma, Virag, Blumer, Moritz, Morales, Ariadna E, Ahmed, Alexis-Walid, Kontopoulos, Dimitrios-Georgios, Hilgers, Leon, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Hiller, Michael, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, and Sullivan, Patrick F

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Female, Mice, Eutheria, Genome, Genomics, Molecular Sequence Annotation, Birds, Zoonomia Consortium‡, General Science & Technology
Abstract

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

Published
2023

9. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Author

Kaplow, Irene M, Lawler, Alyssa J, Schäffer, Daniel E, Srinivasan, Chaitanya, Sestili, Heather H, Wirthlin, Morgan E, Phan, BaDoi N, Prasad, Kavya, Brown, Ashley R, Zhang, Xiaomeng, Foley, Kathleen, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Meyer, Wynn K, Pfenning, Andreas R, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, and Steiner, Cynthia

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Rare Diseases, Congenital Structural Anomalies, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Mental health, Animals, Enhancer Elements, Genetic, Genetic Variation, Machine Learning, Mammals, Phenotype, Zoonomia Consortium**, General Science & Technology
Abstract

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Published
2023

10. Three-dimensional genome rewiring in loci with human accelerated regions

Author

Keough, Kathleen C, Whalen, Sean, Inoue, Fumitaka, Przytycki, Pawel F, Fair, Tyler, Deng, Chengyu, Steyert, Marilyn, Ryu, Hane, Lindblad-Toh, Kerstin, Karlsson, Elinor, Nowakowski, Tomasz, Ahituv, Nadav, Pollen, Alex, Pollard, Katherine S, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Karlsson, Elinor K, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, and Sullivan, Kevin AM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Animals, Humans, Chromatin, Genome, Human, Genomics, Pan troglodytes, Genetic Loci, Neurogenesis, Deep Learning, Zoonomia Consortium§, General Science & Technology
Abstract

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

Published
2023

11. Evolutionary constraint and innovation across hundreds of placental mammals

Author

Christmas, Matthew J, Kaplow, Irene M, Genereux, Diane P, Dong, Michael X, Hughes, Graham M, Li, Xue, Sullivan, Patrick F, Hindle, Allyson G, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Breit, Ana M, Diekhans, Mark, Fanter, Cornelia, Foley, Nicole M, Goodman, Daniel B, Goodman, Linda, Keough, Kathleen C, Kirilenko, Bogdan, Kowalczyk, Amanda, Lawless, Colleen, Lind, Abigail L, Meadows, Jennifer RS, Moreira, Lucas R, Redlich, Ruby W, Ryan, Louise, Swofford, Ross, Valenzuela, Alejandro, Wagner, Franziska, Wallerman, Ola, Brown, Ashley R, Damas, Joana, Fan, Kaili, Gatesy, John, Grimshaw, Jenna, Johnson, Jeremy, Kozyrev, Sergey V, Lawler, Alyssa J, Marinescu, Voichita D, Morrill, Kathleen M, Osmanski, Austin, Paulat, Nicole S, Phan, BaDoi N, Reilly, Steven K, Schäffer, Daniel E, Steiner, Cynthia, Supple, Megan A, Wilder, Aryn P, Wirthlin, Morgan E, Xue, James R, Birren, Bruce W, Gazal, Steven, Hubley, Robert M, Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Meyer, Wynn K, Nweeia, Martin, Sabeti, Pardis C, Shapiro, Beth, Smit, Arian FA, Springer, Mark S, Teeling, Emma C, Weng, Zhiping, Hiller, Michael, Levesque, Danielle L, Lewin, Harris A, Murphy, William J, Navarro, Arcadi, Paten, Benedict, Pollard, Katherine S, Ray, David A, Ruf, Irina, Ryder, Oliver A, Pfenning, Andreas R, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Bredemeyer, Kevin R, Clawson, Hiram, Di Palma, Federica, Eizirik, Eduardo, Forsberg-Nilsson, Karin, Garcia, Carlos J, and Halsey, Michaela K

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Animals, Female, Humans, Conserved Sequence, Eutheria, Evolution, Molecular, Genome, Human, Zoonomia Consortium§, General Science & Technology
Abstract

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Published
2023

12. Evolution of the ancestral mammalian karyotype and syntenic regions

Author

Damas, Joana, Corbo, Marco, Kim, Jaebum, Turner-Maier, Jason, Farré, Marta, Larkin, Denis M, Ryder, Oliver A, Steiner, Cynthia, Houck, Marlys L, Hall, Shaune, Shiue, Lily, Thomas, Stephen, Swale, Thomas, Daly, Mark, Korlach, Jonas, Uliano-Silva, Marcela, Mazzoni, Camila J, Birren, Bruce W, Genereux, Diane P, Johnson, Jeremy, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Nweeia, Martin T, Johnson, Rebecca N, Lewin, Harris A, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, and Ryan, Louise

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Generic health relevance, Animals, Cattle, Chromosomes, Mammalian, Eutheria, Evolution, Molecular, Humans, Karyotype, Mammals, Phylogeny, Sloths, Synteny, chromosome evolution, mammals, synteny conservation, ancestral genome reconstruction, topologically associating domains, Zoonomia Consortium
Abstract

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Published
2022

13. Response to Bakker et al.

Author

Robinson, Jacqueline A, Bowie, Rauri CK, Dudchenko, Olga, Aiden, Erez Lieberman, Hendrickson, Sher L, Steiner, Cynthia C, Ryder, Oliver A, Mindell, David P, and Wall, Jeffrey D

Subjects
Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Robinson and colleagues respond to the points raised about their paper by Bakker et al.

Published
2022

14. Darwinian genomics and diversity in the tree of life

Author

Stephan, Taylorlyn, Burgess, Shawn M, Cheng, Hans, Danko, Charles G, Gill, Clare A, Jarvis, Erich D, Koepfli, Klaus-Peter, Koltes, James E, Lyons, Eric, Ronald, Pamela, Ryder, Oliver A, Schriml, Lynn M, Soltis, Pamela, VandeWoude, Sue, Zhou, Huaijun, Ostrander, Elaine A, and Karlsson, Elinor K

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, History, Heritage and Archaeology, Historical Studies, Biotechnology, Human Genome, Generic health relevance, Animals, Biodiversity, Biological Evolution, Evolution, Molecular, Genetic Variation, Genome, Genomics, Humans, Phylogeny, comparative genomics, evolution, biodiversity, natural models, genomics
Abstract

Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (

Published
2022

15. Why sequence all eukaryotes?

Author

Blaxter, Mark, Archibald, John M, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Di Palma, Federica, Durbin, Richard, Edwards, Scott V, Graves, Jennifer AM, Hackett, Kevin J, Hall, Neil, Jarvis, Erich D, Johnson, Rebecca N, Karlsson, Elinor K, Kress, W John, Kuraku, Shigehiro, Lawniczak, Mara KN, Lindblad-Toh, Kerstin, Lopez, Jose V, Moran, Nancy A, Robinson, Gene E, Ryder, Oliver A, Shapiro, Beth, Soltis, Pamela S, Warnow, Tandy, Zhang, Guojie, and Lewin, Harris A

Subjects
Biotechnology, Animals, Base Sequence, Biodiversity, Biological Evolution, Ecology, Ecosystem, Eukaryota, Genome, Genomics, Humans, Phylogeny, genome, diversity, ecology, evolution, conservation
Abstract

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.

Published
2022

16. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus

Author

Saremi, Nedda F, Oppenheimer, Jonas, Vollmers, Christopher, O’Connell, Brendan, Milne, Shard A, Byrne, Ashley, Yu, Li, Ryder, Oliver A, Green, Richard E, and Shapiro, Beth

Subjects
Biological Sciences, Genetics, Human Genome, Animals, Cell Nucleus, Female, Genome, Molecular Sequence Annotation, Phylogeny, South America, Ursidae, Oxford nanopore, CHiCago, Andean bear, spectacled bear, Tremarctos ornatus, Evolutionary Biology, Evolutionary biology
Abstract

The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.

Published
2021

17. Genome-wide diversity in the California condor tracks its prehistoric abundance and decline

Author

Robinson, Jacqueline A, Bowie, Rauri CK, Dudchenko, Olga, Aiden, Erez Lieberman, Hendrickson, Sher L, Steiner, Cynthia C, Ryder, Oliver A, Mindell, David P, and Wall, Jeffrey D

Subjects
Human Genome, Genetics, Life on Land, Animals, Ecosystem, Endangered Species, Falconiformes, Female, Genome, Genomics, Population Density, conservation, demographic history, extinction, genomics, inbreeding, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America's largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.

Published
2021

18. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide‐Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas‐Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew J, and Jarvis, Erich D

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Life on Land, Animals, Chromosomes, Endangered Species, Female, Genetics, Population, Genome, Phocoena, Conservation genomics, genome diversity, historical demography, Phocoena sinus, porpoise, Vertebrate Genomes Project, Biological Sciences, Evolutionary Biology
Abstract

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2021

19. Platypus and echidna genomes reveal mammalian biology and evolution

Author

Zhou, Yang, Shearwin-Whyatt, Linda, Li, Jing, Song, Zhenzhen, Hayakawa, Takashi, Stevens, David, Fenelon, Jane C, Peel, Emma, Cheng, Yuanyuan, Pajpach, Filip, Bradley, Natasha, Suzuki, Hikoyu, Nikaido, Masato, Damas, Joana, Daish, Tasman, Perry, Tahlia, Zhu, Zexian, Geng, Yuncong, Rhie, Arang, Sims, Ying, Wood, Jonathan, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Li, Qiye, Yang, Huanming, Wang, Jian, Johnston, Stephen D, Phillippy, Adam M, Howe, Kerstin, Jarvis, Erich D, Ryder, Oliver A, Kaessmann, Henrik, Donnelly, Peter, Korlach, Jonas, Lewin, Harris A, Graves, Jennifer, Belov, Katherine, Renfree, Marilyn B, Grutzner, Frank, Zhou, Qi, and Zhang, Guojie

Subjects
Genetics, Human Genome, Biotechnology, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Biological Evolution, Female, Genome, Male, Mammals, Phylogeny, Platypus, Sex Chromosomes, Tachyglossidae, Base Pairing, Base Sequence, Cattle, Chromosome Mapping, Chromosomes, Mammalian, DNA, Evolution, Molecular, Molecular Sequence Data, Mutation, Recombination, Genetic, X Chromosome, Y Chromosome, General Science & Technology
Abstract

Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.

Published
2021

20. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
General Science & Technology
Abstract

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Published
2021

21. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Life on Land, Animals, Birds, Chickens, Conservation of Natural Resources, Datasets as Topic, Finches, Genome, Genomics, Humans, Phylogeny, Selection, Genetic, Synteny, General Science & Technology
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

22. A comparative genomics multitool for scientific discovery and conservation

Author

Genereux, Diane P, Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D, Muren, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R, Chemnick, Leona G, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T, Garber, Manuel, Gladyshev, Vadim N, Goodman, Linda, Haerty, Wilfried, Houck, Marlys L, Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas FK, Lander, Eric S, Meadows, Jennifer RS, Murphy, William J, Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R, Pollard, Katherine S, Ray, David A, Shapiro, Beth, Smit, Arian FA, Springer, Mark S, Steiner, Cynthia C, Swofford, Ross, Taipale, Jussi, Teeling, Emma C, Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A, Lewin, Harris A, Paten, Benedict, Marques-Bonet, Tomas, Lindblad-Toh, Kerstin, and Karlsson, Elinor K

Subjects
Human Genome, Genetics, Biotechnology, Life on Land, Animals, Biodiversity, Biomedical Research, Conservation of Natural Resources, Eutheria, Evolution, Molecular, Extinction, Biological, Genetic Speciation, Genetic Variation, Genomics, Humans, Infections, Knowledge Discovery, Loss of Heterozygosity, Neoplasms, Phylogeny, Risk Assessment, Selection, Genetic, Sequence Alignment, Species Specificity, Venoms, Zoonomia Consortium, General Science & Technology
Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

Published
2020

23. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

Author

Damas, Joana, Hughes, Graham M, Keough, Kathleen C, Painter, Corrie A, Persky, Nicole S, Corbo, Marco, Hiller, Michael, Koepfli, Klaus-Peter, Pfenning, Andreas R, Zhao, Huabin, Genereux, Diane P, Swofford, Ross, Pollard, Katherine S, Ryder, Oliver A, Nweeia, Martin T, Lindblad-Toh, Kerstin, Teeling, Emma C, Karlsson, Elinor K, and Lewin, Harris A

Subjects
Emerging Infectious Diseases, Lung, Prevention, Vaccine Related, Biodefense, Infectious Diseases, Pneumonia, Amino Acids, Animals, Betacoronavirus, Binding Sites, COVID-19, Coronavirus Infections, Evolution, Molecular, Genetic Variation, Host Specificity, Humans, Pandemics, Peptidyl-Dipeptidase A, Pneumonia, Viral, Protein Binding, Receptors, Virus, SARS-CoV-2, Selection, Genetic, Spike Glycoprotein, Coronavirus, Vertebrates, ACE2, comparative genomics, species conservation
Abstract

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency

Published
2020

24. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide-Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas-Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew, and Jarvis, Erich D

Subjects
Human Genome, Genetics, Generic health relevance, Life on Land
Abstract

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2020

25. Precision nomenclature for the new genomics

Author

Lewin, Harris A, Graves, Jennifer A Marshall, Ryder, Oliver A, Graphodatsky, Alexander S, and O'Brien, Stephen J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Philosophy and Religious Studies, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Genome, Genomics, Humans, Terminology as Topic
Abstract

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images of all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclature will assist end users to properly classify genome assemblies, thus facilitating genomic analysis.

Published
2019

26. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

Author

Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A, Kulemzina, Anastasia I, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Graphodatsky, Alexander S, Zhang, Guoije, Larkin, Denis M, and Lewin, Harris A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Life on Land, Animals, Chromosomes, Mammalian, Computational Biology, Evolution, Molecular, Genome, Genomics, Giraffes, High-Throughput Nucleotide Sequencing, Karyotyping, Molecular Sequence Annotation, Phylogeny, giraffe, Giraffa camelopardalis tippelskirchi, assembly, annotation, ruminant, Giraffa camelopardalis tippelskirchi
Abstract

The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes. Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions. We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.

Published
2019

27. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

Author

Lind, Abigail L, Lai, Yvonne YY, Mostovoy, Yulia, Holloway, Alisha K, Iannucci, Alessio, Mak, Angel CY, Fondi, Marco, Orlandini, Valerio, Eckalbar, Walter L, Milan, Massimo, Rovatsos, Michail, Kichigin, Ilya G, Makunin, Alex I, Johnson Pokorná, Martina, Altmanová, Marie, Trifonov, Vladimir A, Schijlen, Elio, Kratochvíl, Lukáš, Fani, Renato, Velenský, Petr, Rehák, Ivan, Patarnello, Tomaso, Jessop, Tim S, Hicks, James W, Ryder, Oliver A, Mendelson, Joseph R, Ciofi, Claudio, Kwok, Pui-Yan, Pollard, Katherine S, and Bruneau, Benoit G

Subjects
Climate Change Impacts and Adaptation, Biological Sciences, Environmental Sciences, Genetics, Human Genome, Cardiovascular, Underpinning research, 1.1 Normal biological development and functioning, Acclimatization, Animals, Cardiovascular System, Chromosomes, Lizards, Ecology, Evolutionary biology, Environmental management
Abstract

Monitor lizards are unique among ectothermic reptiles in that they have high aerobic capacity and distinctive cardiovascular physiology resembling that of endothermic mammals. Here, we sequence the genome of the Komodo dragon Varanus komodoensis, the largest extant monitor lizard, and generate a high-resolution de novo chromosome-assigned genome assembly for V. komodoensis using a hybrid approach of long-range sequencing and single-molecule optical mapping. Comparing the genome of V. komodoensis with those of related species, we find evidence of positive selection in pathways related to energy metabolism, cardiovascular homoeostasis, and haemostasis. We also show species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and other lizard lineages. Together, these evolutionary signatures of adaptation reveal the genetic underpinnings of the unique Komodo dragon sensory and cardiovascular systems, and suggest that selective pressure altered haemostasis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. The Komodo dragon genome is an important resource for understanding the biology of monitor lizards and reptiles worldwide.

Published
2019

28. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Author

Farré, Marta, Kim, Jaebum, Proskuryakova, Anastasia A, Zhang, Yang, Kulemzina, Anastasia I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L, Perelman, Polina L, Johnson, Warren E, Warren, Wesley C, Kukekova, Anna V, Zhang, Guojie, O'Brien, Stephen J, Ryder, Oliver A, Graphodatsky, Alexander S, Ma, Jian, Lewin, Harris A, and Larkin, Denis M

Subjects
Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Animals, Chromosome Breakpoints, DNA Transposable Elements, Enhancer Elements, Genetic, Evolution, Molecular, Karyotype, Protein Binding, Ruminants, Selection, Genetic, Synteny, Transcription Factors, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.

Published
2019

29. A Near-Chromosome-Scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari Desert

Author

Farré, Marta, Li, Qiye, Zhou, Yang, Damas, Joana, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Zhang, Guojie, Larkin, Denis M, and Lewin, Harris A

Subjects
Human Genome, Genetics, Animals, Antelopes, Female, Genome, Genomics, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Phylogeny, Sequence Analysis, DNA, gemsbok, Oryx gazella, assembly, annotation, ruminant, drought
Abstract

The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions. Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.

Published
2019

31. Unraveling the genomic diversity and admixture history of captive tigers in the United States.

Author

Armstrong, Ellie E., Mooney, Jazlyn A., Solari, Katherine A., Kim, Bernard Y., Barsh, Gregory S., Grant, Victoria B., Greenbaum, Gili, Kaelin, Christopher B., Panchenko, Katya, Pickrell, Joseph K., Rosenberg, Noah, Ryder, Oliver A., Tsuya Yokoyama, Ramakrishnan, Uma, Petrov, Dmitri A., and Hadly, Elizabeth A.

Subjects
TIGERS, WHOLE genome sequencing, ENDANGERED species, GENETIC variation, CONSERVATION projects (Natural resources)
Abstract

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (Panthera tigris), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25×) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex-and in situ populations. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

34. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C., Lama, Tanya M., Grutzner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich, III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E., Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., and Jarvis, Erich D.

Published
2021
Full Text
View/download PDF

35. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.

Author

Tomaszkiewicz, Marta, Rangavittal, Samarth, Cechova, Monika, Campos Sanchez, Rebeca, Fescemyer, Howard, Harris, Robert, Ye, Danling, OBrien, Patricia, Chikhi, Rayan, Ryder, Oliver, Ferguson-Smith, Malcolm, Medvedev, Paul, and Makova, Kateryna

Subjects
Animals, Computational Biology, Gene Rearrangement, Genome, Genomics, Gorilla gorilla, High-Throughput Nucleotide Sequencing, Humans, Inverted Repeat Sequences, Male, Mammals, Microsatellite Repeats, Pan troglodytes, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Y Chromosome
Abstract

The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.

Published
2016

36. Endangered Przewalski's horse, Equus pzrewalskii, cloned from historically cryopreserved cells

Author

Novak, Ben Jacob, primary, Ryder, Oliver A, additional, Houck, Marlys L, additional, Putnam, Andrea S, additional, Walker, Kelcey, additional, Russell, Lexie, additional, Russell, Blake, additional, Walker, Shawn, additional, Arenivas, Sanaz Sadeghieh, additional, Aston, Lauren, additional, Veneklasen, Gregg, additional, Ivy, Jamie A, additional, Koepfli, Klaus-Peter, additional, Rusnak, Anna, additional, Simek, Jaroslav, additional, Zhuk, Anna, additional, and Phelan, Ryan, additional

Published
2023
Full Text
View/download PDF

37. Data gaps and opportunities for comparative and conservation biology

Author

Conde, Dalia A., Staerk, Johanna, Colchero, Fernando, da Silva, Rita, Schöley, Jonas, Baden, H. Maria, Jouvet, Lionel, Fa, John E., Syed, Hassan, Jongejans, Eelke, Meiri, Shai, Gaillard, Jean-Michel, Chamberlain, Scott, Wilcken, Jonathan, Jones, Owen R., Dahlgren, Johan P., Steiner, Ulrich K., Bland, Lucie M., Gomez-Mestre, Ivan, Lebreton, Jean-Dominique, Vargas, Jaime González, Flesness, Nate, Canudas-Romo, Vladimir, Salguero-Gómez, Roberto, Byers, Onnie, Berg, Thomas Bjørneboe, Scheuerlein, Alexander, Devillard, Sébastien, Schigel, Dmitry S., Ryder, Oliver A., Possingham, Hugh P., Baudisch, Annette, and Vaupel, James W.

Published
2019

39. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Author

von Seth, Johanna, Dussex, Nicolas, Díez-del-Molino, David, van der Valk, Tom, Kutschera, Verena E., Kierczak, Marcin, Steiner, Cynthia C., Liu, Shanlin, Gilbert, M. Thomas P., Sinding, Mikkel-Holger S., Prost, Stefan, Guschanski, Katerina, Nathan, Senthilvel K. S. S., Brace, Selina, Chan, Yvonne L., Wheat, Christopher W., Skoglund, Pontus, Ryder, Oliver A., Goossens, Benoit, Götherström, Anders, and Dalén, Love

Published
2021
Full Text
View/download PDF

42. Extreme selective sweeps independently targeted the X chromosomes of the great apes

Author

Nam, Kiwoong, Munch, Kasper, Hobolth, Asger, Dutheil, Julien Yann, Veeramah, Krishna R, Woerner, August E, Hammer, Michael F, Mailund, Thomas, Schierup, Mikkel Heide, Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, O’Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Human Genome, Genetics, Animals, Computational Biology, Databases, Genetic, Genetic Variation, Genetics, Population, Hominidae, Models, Genetic, Polymorphism, Genetic, Selection, Genetic, Species Specificity, X Chromosome, Great Ape Genome Diversity Project, X-chromosome evolution, ampliconic genes, great apes, meiotic drive, selective sweeps
Abstract

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.

Published
2015

43. 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

44. 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

45. The birds of Genome10K

Author

OBrien, Stephen J, Haussler, David, and Ryder, Oliver

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Birds, Aves, Avian, Vertebrate, Genomics, Genome10K, Phylogenomics, Avian phylogenomics project
Abstract

Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers - both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science, Genome Biology and GigaScience (which also included pre-publication data release). These present the successful beginnings of an international interdisciplinary venture, the Avian Phylogenomics Project that lets us view, through a genomics lens, modern bird species and the evolutionary events that produced them.

Published
2014

46. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author

Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Published
2022
Full Text
View/download PDF

48. A comprehensive genomic history of extinct and living elephants

Author

Palkopoulou, Eleftheria, Lipson, Mark, Mallick, Swapan, Nielsen, Svend, Rohland, Nadin, Baleka, Sina, Karpinski, Emil, Ivancevic, Atma M., To, Thu-Hien, Kortschak, R. Daniel, Raison, Joy M., Qu, Zhipeng, Chin, Tat-Jun, Alt, Kurt W., Claesson, Stefan, Dalén, Love, MacPhee, Ross D. E., Meller, Harald, Roca, Alfred L., Ryder, Oliver A., Heiman, David, Young, Sarah, Breen, Matthew, Williams, Christina, Aken, Bronwen L., Ruffier, Magali, Karlsson, Elinor, Johnson, Jeremy, Di Palma, Federica, Alfoldi, Jessica, Adelson, David L., Mailund, Thomas, Munch, Kasper, Lindblad-Toh, Kerstin, Hofreiter, Michael, Poinar, Hendrik, and Reich, David

Published
2018

50. BRIEF REPORT 9.1

Author

Zhang, Yunwu, primary, Zhang, Hemin, additional, Zhang, Guiquan, additional, Ryder, Oliver A., additional, and Zhang, Yaping, additional

Published
2019
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results