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49 results on '"Steiner, Cynthia C"'

2. 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

3. 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

4. Highly accurate long-read HiFi sequencing data for five complex genomes.

Author

Hon, Ting, Mars, Kristin, Young, Greg, Tsai, Yu-Chih, Karalius, Joseph W, Landolin, Jane M, Maurer, Nicholas, Kudrna, David, Hardigan, Michael A, Steiner, Cynthia C, Knapp, Steven J, Ware, Doreen, Shapiro, Beth, Peluso, Paul, and Rank, David R

Abstract

The PacBio® HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.

Published
2020

5. 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

7. 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
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11. A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

Author

Wilder, Aryn P, primary, Dudchenko, Olga, additional, Curry, Caitlin, additional, Korody, Marisa, additional, Turbek, Sheela P, additional, Daly, Mark, additional, Misuraca, Ann, additional, Wang, Gaojianyong, additional, Khan, Ruqayya, additional, Weisz, David, additional, Fronczek, Julie, additional, Aiden, Erez Lieberman, additional, Houck, Marlys L, additional, Shier, Debra M, additional, Ryder, Oliver A, additional, and Steiner, Cynthia C, additional

Published
2022
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12. Corrigendum to: Facultative Parthenogenesis in California Condors

Author

Ryder, Oliver A., Thomas, Steven, Martin Judson, Jessica, Romanov, Michael N., Dandekar, Sugandha, Papp, Jeanette C., Sidak-Loftis, Lindsay C., Walker, Kelli, Stalis, Ilse H., Mace, Michael, Steiner, Cynthia C., Chemnick, Leona G., Ryder, Oliver A., Thomas, Steven, Martin Judson, Jessica, Romanov, Michael N., Dandekar, Sugandha, Papp, Jeanette C., Sidak-Loftis, Lindsay C., Walker, Kelli, Stalis, Ilse H., Mace, Michael, Steiner, Cynthia C., and Chemnick, Leona G.

Abstract

This is a correction to: Journal of Heredity, Volume 112, Issue 7, October 2021, Pages 569–574, https://doi.org/10.1093/jhered/esab052 In the originally published version of this article there were errors within an author’s affiliations. The author names for Conservation Genetics, Beckman Center for Conservation Research should read: “Ryder, Thomas, Judson, Sidak-Loftis, Steiner, and Chemnick” instead of (Ryder, Thomas, Judson, Romanov, Sidak-Loftis, Steiner, and Chemnick”. The author names for San Diego Zoo Wildlife Alliance should read: “Mace, Romanov” instead of “Mace”. These errors have now been corrected online.

Published
2022

13. Corrigendum to: Facultative Parthenogenesis in California Condors

Author

Ryder, Oliver A, primary, Thomas, Steven, additional, Judson, Jessica Martin, additional, Romanov, Michael N, additional, Dandekar, Sugandha, additional, Papp, Jeanette C, additional, Sidak-Loftis, Lindsay C, additional, Walker, Kelli, additional, Stalis, Ilse H, additional, Mace, Michael, additional, Steiner, Cynthia C, additional, and Chemnick, Leona G, additional

Published
2021
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15. Facultative Parthenogenesis in California Condors

Author

Ryder, Oliver A, primary, Thomas, Steven, additional, Judson, Jessica Martin, additional, Romanov, Michael N, additional, Dandekar, Sugandha, additional, Papp, Jeanette C, additional, Sidak-Loftis, Lindsay C, additional, Walker, Kelli, additional, Stalis, Ilse H, additional, Mace, Michael, additional, Steiner, Cynthia C, additional, and Chemnick, Leona G, additional

Published
2021
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17. Facultative parthenogenesis in California condors

Author

Ryder, Oliver A, Thomas, Steven, Martin Judson, Jessica, Romanov, Michael N, Dandekar, Sugandha, Papp, Jeanette C., Sidak-Loftis, Lindsay C., Walker, Kelli, Stalis, Ilse H., Mace, Michael, Steiner, Cynthia C, Chemnick, Leona G., Ryder, Oliver A, Thomas, Steven, Martin Judson, Jessica, Romanov, Michael N, Dandekar, Sugandha, Papp, Jeanette C., Sidak-Loftis, Lindsay C., Walker, Kelli, Stalis, Ilse H., Mace, Michael, Steiner, Cynthia C, and Chemnick, Leona G.

Abstract

Parthenogenesis is a relatively rare event in birds, documented in unfertilized eggs from columbid, galliform, and passerine females with no access to males. In the critically endangered California condor, parentage analysis conducted utilizing polymorphic microsatellite loci has identified two instances of parthenogenetic development from the eggs of two females in the captive breeding program, each continuously housed with a reproductively capable male with whom they had produced offspring. Paternal genetic contribution to the two chicks was excluded. Both parthenotes possessed the expected male ZZ sex chromosomes and were homozygous for all evaluated markers inherited from their dams. These findings represent the first molecular marker-based identification of facultative parthenogenesis in an avian species, notably of females in regular contact with fertile males, and add to the phylogenetic breadth of vertebrate taxa documented to have reproduced via asexual reproduction.

Published
2021

18. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Author

Science for Life Laboratory, Garvan Institute of Medical Research, Knut and Alice Wallenberg Foundation, Swedish Research Council, European Research Council, Independent Research Fund Denmark, Australian Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Liu, Shanlin, Westbury, Michael V., Dussex, Nicolas, Mitchell, Kieren J., Sinding, Mikkel-Holger S., Heintzman, Peter D., Duchêne, David A., Kapp, Joshua D., von Seth, Johanna, Heiniger, Holly, Sánchez-Barreiro, Fátima, Margaryan, Ashot, André-Olsen, Remi, Cahsan, Binia de, Meng, Guanliang, Yang, Chentao, Chen, Lei, van der Valk, Tom, Moodley, Yoshan, Rookmaaker, Kees, Bruford, Michael W., Ryder, Oliver A., Steiner, Cynthia C., Bruins-van Sonsbeek, Linda G. R., Vartanyan, Sergey, Guo, Chunxue, Cooper, Alan, Kosintsev, Pavel, Kirillova, Irina, Lister, Adrian M., Marqués-Bonet, Tomàs, Gopalakrishnan, Shyam, Dunn, Robert R., Lorenzen, Eline D., Shapiro, Beth, Zhang, Guojie, Antoine, Pierre-Olivier, Dalén, Love, Gilbert, M. Thomas P., Science for Life Laboratory, Garvan Institute of Medical Research, Knut and Alice Wallenberg Foundation, Swedish Research Council, European Research Council, Independent Research Fund Denmark, Australian Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Liu, Shanlin, Westbury, Michael V., Dussex, Nicolas, Mitchell, Kieren J., Sinding, Mikkel-Holger S., Heintzman, Peter D., Duchêne, David A., Kapp, Joshua D., von Seth, Johanna, Heiniger, Holly, Sánchez-Barreiro, Fátima, Margaryan, Ashot, André-Olsen, Remi, Cahsan, Binia de, Meng, Guanliang, Yang, Chentao, Chen, Lei, van der Valk, Tom, Moodley, Yoshan, Rookmaaker, Kees, Bruford, Michael W., Ryder, Oliver A., Steiner, Cynthia C., Bruins-van Sonsbeek, Linda G. R., Vartanyan, Sergey, Guo, Chunxue, Cooper, Alan, Kosintsev, Pavel, Kirillova, Irina, Lister, Adrian M., Marqués-Bonet, Tomàs, Gopalakrishnan, Shyam, Dunn, Robert R., Lorenzen, Eline D., Shapiro, Beth, Zhang, Guojie, Antoine, Pierre-Olivier, Dalén, Love, and Gilbert, M. Thomas P.

Abstract

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Published
2021

20. Correcting parentage relationships in the endangered California Condor: Improving mean kinship estimates for conservation management

Author

Moran, Brigid M, primary, Thomas, Steven M, additional, Judson, Jessica M, additional, Navarro, Asako, additional, Davis, Heidi, additional, Sidak-Loftis, Lindsay, additional, Korody, Marisa, additional, Mace, Michael, additional, Ralls, Katherine, additional, Callicrate, Taylor, additional, Ryder, Oliver A, additional, Chemnick, Leona G, additional, and Steiner, Cynthia C, additional

Published
2021
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21. Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.

Author

Wilder, Aryn P, Dudchenko, Olga, Curry, Caitlin, Korody, Marisa, Turbek, Sheela P, Daly, Mark, Misuraca, Ann, Wang, Gaojianyong, Khan, Ruqayya, Weisz, David, Fronczek, Julie, Aiden, Erez Lieberman, Houck, Marlys L, Shier, Debra M, Ryder, Oliver A, and Steiner, Cynthia C

Subjects
GENETIC load, MITOCHONDRIAL DNA, INBREEDING, GENOMES, GENETIC variation, BIODIVERSITY conservation
Abstract

High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load. [ABSTRACT FROM AUTHOR]

Published
2022
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22. A comparative genomics multitool for scientific discovery and conservation

Author

Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita, Murén, 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 F. K., Lander, Eric S., Meadows, Jennifer, Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., 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, Karlsson, Elinor K., Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita, Murén, 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 F. K., Lander, Eric S., Meadows, Jennifer, Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., 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.

Abstract

A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. 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., Group Authors: Zoonomia Consortium

Published
2020
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23. A comparative genomics multitool for scientific discovery and conservation

Author

National Institutes of Health (US), Swedish Research Council, Knut and Alice Wallenberg Foundation, Uppsala University, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Howard Hughes Medical Institute, European Research Council, Fundación la Caixa, Wellcome Trust, Royal Society (UK), Ministerio de Economía y Competitividad (España), Fondation Prince Albert II de Monaco, Smithsonian Institution, Irish Research Council, Medical Research Council (UK), National Science Foundation (US), Academy of Finland, Genereux, Diane P., Serres-Armero, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Murén, 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 F. K., Lander, Eric S., Meadows, Jennifer R.S., Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., 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, Marqués-Bonet, Tomàs, Lindblad-Toh, Kerstin, Karlsson, Elinor K., National Institutes of Health (US), Swedish Research Council, Knut and Alice Wallenberg Foundation, Uppsala University, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Howard Hughes Medical Institute, European Research Council, Fundación la Caixa, Wellcome Trust, Royal Society (UK), Ministerio de Economía y Competitividad (España), Fondation Prince Albert II de Monaco, Smithsonian Institution, Irish Research Council, Medical Research Council (UK), National Science Foundation (US), Academy of Finland, Genereux, Diane P., Serres-Armero, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Murén, 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 F. K., Lander, Eric S., Meadows, Jennifer R.S., Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., 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, Marqués-Bonet, Tomàs, Lindblad-Toh, Kerstin, and Karlsson, Elinor K.

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

24. Highly accurate long-read HiFi sequencing data for five complex genomes

Author

Hon, Ting, primary, Mars, Kristin, additional, Young, Greg, additional, Tsai, Yu-Chih, additional, Karalius, Joseph W., additional, Landolin, Jane M., additional, Maurer, Nicholas, additional, Kudrna, David, additional, Hardigan, Michael A., additional, Steiner, Cynthia C., additional, Knapp, Steven J., additional, Ware, Doreen, additional, Shapiro, Beth, additional, Peluso, Paul, additional, and Rank, David R., additional

Published
2020
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26. The sequence and de novo assembly of the giant panda genome

Author

Li, Ruiqiang, Fan, Wei, Tian, Geng, Zhu, Hongmei, He, Lin, Cai, Jing, Huang, Quanfei, Cai, Qingle, Li, Bo, Bai, Yinqi, Zhang, Zhihe, Zhang, Yaping, Wang, Wen, Li, Jun, Wei, Fuwen, Li, Heng, Jian, Min, Li, Jianwen, Zhang, Zhaolei, Nielsen, Rasmus, Li, Dawei, Gu, Wanjun, Yang, Zhentao, Xuan, Zhaoling, Ryder, Oliver A., Leung, Frederick Chi-Ching, Zhou, Yan, Cao, Jianjun, Sun, Xiao, Fu, Yonggui, Fang, Xiaodong, Guo, Xiaosen, Wang, Bo, Hou, Rong, Shen, Fujun, Mu, Bo, Ni, Peixiang, Lin, Runmao, Qian, Wubin, Wang, Guodong, Yu, Chang, Nie, Wenhui, Wang, Jinhuan, Wu, Zhigang, Liang, Huiqing, Min, Jiumeng, Wu, Qi, Cheng, Shifeng, Ruan, Jue, Wang, Mingwei, Shi, Zhongbin, Wen, Ming, Liu, Binghang, Ren, Xiaoli, Zheng, Huisong, Dong, Dong, Cook, Kathleen, Shan, Gao, Zhang, Hao, Kosiol, Carolin, Xie, Xueying, Lu, Zuhong, Zheng, Hancheng, Li, Yingrui, Steiner, Cynthia C., Lam, Tommy Tsan-Yuk, Lin, Siyuan, Zhang, Qinghui, Li, Guoqing, Tian, Jing, Gong, Timing, Liu, Hongde, Zhang, Dejin, Fang, Lin, Ye, Chen, Zhang, Juanbin, Hu, Wenbo, Xu, Anlong, Ren, Yuanyuan, Zhang, Guojie, Bruford, Michael W., Li, Qibin, Ma, Lijia, Guo, Yiran, An, Na, Hu, Yujie, Zheng, Yang, Shi, Yongyong, Li, Zhiqiang, Liu, Qing, Chen, Yanling, Zhao, Jing, Qu, Ning, Zhao, Shancen, Tian, Feng, Wang, Xiaoling, Wang, Haiyin, Xu, Lizhi, Liu, Xiao, Vinar, Tomas, Wang, Yajun, Lam, Tak-Wah, Yiu, Siu-Ming, Liu, Shiping, Zhang, Hemin, Li, Desheng, Huang, Yan, Wang, Xia, Yang, Guohua, Jiang, Zhi, Wang, Junyi, Qin, Nan, Li, Li, Li, Jingxiang, Bolund, Lars, Kristiansen, Karsten, Wong, Gane Ka-Shu, Olson, Maynard, Zhang, Xiuqing, Li, Songgang, Yang, Huanming, Wang, Jian, and Wang, Jun

Published
2010
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28. New World Monkey Resembles Human in Bitter Taste Receptor Evolution and Function via a Single Parallel Amino Acid Substitution.

Author

Yang, Hui, Yang, Songlin, Fan, Fei, Li, Yun, Dai, Shaoxing, Zhou, Xin, Steiner, Cynthia C, Coppedge, Bretton, Roos, Christian, Cai, Xianghai, Irwin, David M, and Shi, Peng

Subjects
BITTERNESS (Taste), TASTE receptors, AMINO acids, WHITE-faced saki, GLYCOSIDES
Abstract

Bitter taste receptors serve as a vital component in the defense system against toxin intake by animals, and the family of genes encoding these receptors has been demonstrated, usually by family size variance, to correlate with dietary preference. However, few systematic studies of specific Tas2R to unveil their functional evolution have been conducted. Here, we surveyed Tas2R16 across all major clades of primates and reported a rare case of a convergent change to increase sensitivity to β-glucopyranosides in human and a New World monkey, the white-faced saki. Combining analyses at multiple levels, we demonstrate that a parallel amino acid substitution (K172N) shared by these two species is responsible for this functional convergence of Tas2R16. Considering the specialized feeding preference of the white-faced saki, the K172N change likely played an important adaptive role in its early evolution to avoid potentially toxic cyanogenic glycosides, as suggested for the human TAS2R16 gene. [ABSTRACT FROM AUTHOR]

Published
2021
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29. A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii’s Last Remaining Crow Species

Author

Sutton, Jolene T., primary, Helmkampf, Martin, additional, Steiner, Cynthia C., additional, Bellinger, M. Renee, additional, Korlach, Jonas, additional, Hall, Richard, additional, Baybayan, Primo, additional, Muehling, Jill, additional, Gu, Jenny, additional, Kingan, Sarah, additional, Masuda, Bryce M., additional, and Ryder, Oliver A., additional

Published
2018
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31. Whole genome sequencing of California condors is now utilized for guiding genetic management

Author

Ryder, Oliver, Miller, Webb, Ralls, Katherine, Ballou, Jonathan D, Steiner, Cynthia C, Mitelberg, Anna, Romanov, Michael N, Chemnick, Leona G, Mace, Michael, and Schuster, Stephan

Subjects
QL, QH75, QH426
Abstract

The California condor is a critically endangered avian species that, in 1982, became extinct in the wild. Its survival has persevered through a captive breeding program and reintroduction efforts within its former range. As of April, 2015, 421 California condors, including 204 flying in the wild constituted the extant population. Concern regarding preservation of genetic diversity and inbreeding, have led to intensive population management supported by molecular genetics research and, more recently, the application of genomic methodologies. 36 complete California condor genomes, representing the whole gene pool of the species, have been sequenced identifying about 4 millions polymorphic sites (SNPs). This has allowed reassessment of kinship among the founder birds, which is now being applied to selecting breeding pairs for the ongoing captive propagation effort. A genetic disease, chondrodystrophy, is inherited consistent with an autosomal recessive mode of transmission in condors. Utilizing whole genome sequencing of affected chicks and their carrier parents, a series of linked markers localized in a 1 Mb region of the condor genome have been employed to detect carrier condors heterozygous for the lethal mutation. This information can be incorporated into population management to reduce the risk of reproductive failure, as reintroduced populations begin to expand.

Published
2016

33. Whole genome sequencing of California condors is now utilized for guiding genetic management

Author

Ryder, Oliver A., Miller, Webb, Ralls, Katherine, Ballou, Jonathan D, Steiner, Cynthia C, Mitelberg, Anna, Romanov, Michael N, Chemnick, Leona G., Mace, Michael, Schuster, Stephan, Ryder, Oliver A., Miller, Webb, Ralls, Katherine, Ballou, Jonathan D, Steiner, Cynthia C, Mitelberg, Anna, Romanov, Michael N, Chemnick, Leona G., Mace, Michael, and Schuster, Stephan

Abstract

The California condor is a critically endangered avian species that, in 1982, became extinct in the wild. Its survival has persevered through a captive breeding program and reintroduction efforts within its former range. As of April, 2015, 421 California condors, including 204 flying in the wild constituted the extant population. Concern regarding preservation of genetic diversity and inbreeding, have led to intensive population management supported by molecular genetics research and, more recently, the application of genomic methodologies. 36 complete California condor genomes, representing the whole gene pool of the species, have been sequenced identifying about 4 millions polymorphic sites (SNPs). This has allowed reassessment of kinship among the founder birds, which is now being applied to selecting breeding pairs for the ongoing captive propagation effort. A genetic disease, chondrodystrophy, is inherited consistent with an autosomal recessive mode of transmission in condors. Utilizing whole genome sequencing of affected chicks and their carrier parents, a series of linked markers localized in a 1 Mb region of the condor genome have been employed to detect carrier condors heterozygous for the lethal mutation. This information can be incorporated into population management to reduce the risk of reproductive failure, as reintroduced populations begin to expand.

Published
2016

34. Molecular phylogeny and evolution of the Perissodactyla

Author

Steiner, Cynthia C. and Ryder, Oliver A.

Subjects
Biodiversity, Taxonomy
Abstract

Steiner, Cynthia C., Ryder, Oliver A. (2011): Molecular phylogeny and evolution of the Perissodactyla. Zoological Journal of the Linnean Society 163 (4): 1289-1303, DOI: 10.1111/j.1096-3642.2011.00752.x, URL: http://dx.doi.org/10.1111/j.1096-3642.2011.00752.x

Published
2011

42. Erratum: The sequence and de novo assembly of the giant panda genome

Author

Li, Ruiqiang, primary, Fan, Wei, additional, Tian, Geng, additional, Zhu, Hongmei, additional, He, Lin, additional, Cai, Jing, additional, Huang, Quanfei, additional, Cai, Qingle, additional, Li, Bo, additional, Bai, Yinqi, additional, Zhang, Zhihe, additional, Zhang, Yaping, additional, Wang, Wen, additional, Li, Jun, additional, Wei, Fuwen, additional, Li, Heng, additional, Jian, Min, additional, Li, Jianwen, additional, Zhang, Zhaolei, additional, Nielsen, Rasmus, additional, Li, Dawei, additional, Gu, Wanjun, additional, Yang, Zhentao, additional, Xuan, Zhaoling, additional, Ryder, Oliver A., additional, Leung, Frederick Chi-Ching, additional, Zhou, Yan, additional, Cao, Jianjun, additional, Sun, Xiao, additional, Fu, Yonggui, additional, Fang, Xiaodong, additional, Guo, Xiaosen, additional, Wang, Bo, additional, Hou, Rong, additional, Shen, Fujun, additional, Mu, Bo, additional, Ni, Peixiang, additional, Lin, Runmao, additional, Qian, Wubin, additional, Wang, Guodong, additional, Yu, Chang, additional, Nie, Wenhui, additional, Wang, Jinhuan, additional, Wu, Zhigang, additional, Liang, Huiqing, additional, Min, Jiumeng, additional, Wu, Qi, additional, Cheng, Shifeng, additional, Ruan, Jue, additional, Wang, Mingwei, additional, Shi, Zhongbin, additional, Wen, Ming, additional, Liu, Binghang, additional, Ren, Xiaoli, additional, Zheng, Huisong, additional, Dong, Dong, additional, Cook, Kathleen, additional, Shan, Gao, additional, Zhang, Hao, additional, Kosiol, Carolin, additional, Xie, Xueying, additional, Lu, Zuhong, additional, Zheng, Hancheng, additional, Li, Yingrui, additional, Steiner, Cynthia C., additional, Lam, Tommy Tsan-Yuk, additional, Lin, Siyuan, additional, Zhang, Qinghui, additional, Li, Guoqing, additional, Tian, Jing, additional, Gong, Timing, additional, Liu, Hongde, additional, Zhang, Dejin, additional, Fang, Lin, additional, Ye, Chen, additional, Zhang, Juanbin, additional, Hu, Wenbo, additional, Xu, Anlong, additional, Ren, Yuanyuan, additional, Zhang, Guojie, additional, Bruford, Michael W., additional, Li, Qibin, additional, Ma, Lijia, additional, Guo, Yiran, additional, An, Na, additional, Hu, Yujie, additional, Zheng, Yang, additional, Shi, Yongyong, additional, Li, Zhiqiang, additional, Liu, Qing, additional, Chen, Yanling, additional, Zhao, Jing, additional, Qu, Ning, additional, Zhao, Shancen, additional, Tian, Feng, additional, Wang, Xiaoling, additional, Wang, Haiyin, additional, Xu, Lizhi, additional, Liu, Xiao, additional, Vinar, Tomas, additional, Wang, Yajun, additional, Lam, Tak-Wah, additional, Yiu, Siu-Ming, additional, Liu, Shiping, additional, Zhang, Hemin, additional, Li, Desheng, additional, Huang, Yan, additional, Wang, Xia, additional, Yang, Guohua, additional, Jiang, Zhi, additional, Wang, Junyi, additional, Qin, Nan, additional, Li, Li, additional, Li, Jingxiang, additional, Bolund, Lars, additional, Kristiansen, Karsten, additional, Wong, Gane Ka-Shu, additional, Olson, Maynard, additional, Zhang, Xiuqing, additional, Li, Songgang, additional, Yang, Huanming, additional, Wang, Jian, additional, and Wang, Jun, additional

Published
2010
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43. The sequence and de novo assembly of the giant panda genome

Author

Li, Ruiqiang, primary, Fan, Wei, additional, Tian, Geng, additional, Zhu, Hongmei, additional, He, Lin, additional, Cai, Jing, additional, Huang, Quanfei, additional, Cai, Qingle, additional, Li, Bo, additional, Bai, Yinqi, additional, Zhang, Zhihe, additional, Zhang, Yaping, additional, Wang, Wen, additional, Li, Jun, additional, Wei, Fuwen, additional, Li, Heng, additional, Jian, Min, additional, Li, Jianwen, additional, Zhang, Zhaolei, additional, Nielsen, Rasmus, additional, Li, Dawei, additional, Gu, Wanjun, additional, Yang, Zhentao, additional, Xuan, Zhaoling, additional, Ryder, Oliver A., additional, Leung, Frederick Chi-Ching, additional, Zhou, Yan, additional, Cao, Jianjun, additional, Sun, Xiao, additional, Fu, Yonggui, additional, Fang, Xiaodong, additional, Guo, Xiaosen, additional, Wang, Bo, additional, Hou, Rong, additional, Shen, Fujun, additional, Mu, Bo, additional, Ni, Peixiang, additional, Lin, Runmao, additional, Qian, Wubin, additional, Wang, Guodong, additional, Yu, Chang, additional, Nie, Wenhui, additional, Wang, Jinhuan, additional, Wu, Zhigang, additional, Liang, Huiqing, additional, Min, Jiumeng, additional, Wu, Qi, additional, Cheng, Shifeng, additional, Ruan, Jue, additional, Wang, Mingwei, additional, Shi, Zhongbin, additional, Wen, Ming, additional, Liu, Binghang, additional, Ren, Xiaoli, additional, Zheng, Huisong, additional, Dong, Dong, additional, Cook, Kathleen, additional, Shan, Gao, additional, Zhang, Hao, additional, Kosiol, Carolin, additional, Xie, Xueying, additional, Lu, Zuhong, additional, Zheng, Hancheng, additional, Li, Yingrui, additional, Steiner, Cynthia C., additional, Lam, Tommy Tsan-Yuk, additional, Lin, Siyuan, additional, Zhang, Qinghui, additional, Li, Guoqing, additional, Tian, Jing, additional, Gong, Timing, additional, Liu, Hongde, additional, Zhang, Dejin, additional, Fang, Lin, additional, Ye, Chen, additional, Zhang, Juanbin, additional, Hu, Wenbo, additional, Xu, Anlong, additional, Ren, Yuanyuan, additional, Zhang, Guojie, additional, Bruford, Michael W., additional, Li, Qibin, additional, Ma, Lijia, additional, Guo, Yiran, additional, An, Na, additional, Hu, Yujie, additional, Zheng, Yang, additional, Shi, Yongyong, additional, Li, Zhiqiang, additional, Liu, Qing, additional, Chen, Yanling, additional, Zhao, Jing, additional, Qu, Ning, additional, Zhao, Shancen, additional, Tian, Feng, additional, Wang, Xiaoling, additional, Wang, Haiyin, additional, Xu, Lizhi, additional, Liu, Xiao, additional, Vinar, Tomas, additional, Wang, Yajun, additional, Lam, Tak-Wah, additional, Yiu, Siu-Ming, additional, Liu, Shiping, additional, Zhang, Hemin, additional, Li, Desheng, additional, Huang, Yan, additional, Wang, Xia, additional, Yang, Guohua, additional, Jiang, Zhi, additional, Wang, Junyi, additional, Qin, Nan, additional, Li, Li, additional, Li, Jingxiang, additional, Bolund, Lars, additional, Kristiansen, Karsten, additional, Wong, Gane Ka-Shu, additional, Olson, Maynard, additional, Zhang, Xiuqing, additional, Li, Songgang, additional, Yang, Huanming, additional, Wang, Jian, additional, and Wang, Jun, additional

Published
2009
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47. Characterization of Prdm9 in Equids and Sterility in Mules.

Author

Steiner, Cynthia C. and Ryder, Oliver A.

Subjects
*MULES, *ANIMAL infertility, *GAMETOGENESIS, *ANIMAL species, *MOLECULAR genetics, *SPERMATOGENESIS in animals, *HISTONE methyltransferases, *NATURAL selection, *COMPARATIVE genomics, REPRODUCTIVE isolation
Abstract

: Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy’s zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility. [ABSTRACT FROM AUTHOR]

Published
2013
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48. Species identification and chromosome variation of captive two-toed sloths.

Author

Steiner, Cynthia C., Houck, Marlys L., and Ryder, Oliver A.

Abstract

Two-toed sloth species, Linnaeus's and Hoffmman's, are frequent residents of zoo collections in North America. However, species identification has always been problematic because of their large overlap in external morphology, which represents an obstacle to the captive breeding program. We describe here a PCR-based technique that allows species identification of two-toed sloths without requiring sequencing, by using a mitochondrial marker ( COI gene) and restriction enzyme assay. We also report intra- and inter-specific patterns of chromosome variation in captive two-toed sloths. Molecularly, we identified 22 samples of Linnaeus's and Hoffmman's two-toed sloths corresponding to 14 and 8 individuals, respectively. One animal was identified as a hybrid using the nuclear gene Enam having alleles derived from both species. The chromosome number in Hoffman's two-toed sloths showed low variation ranging only between 50 and 51. In contrast, Linnaeus's two-toed sloths appeared to vary widely, with diploid numbers ranging from 53 to 67, suggesting distinct geographic groups. The species identification method presented here represents a low-cost easy-to-use tool that will help to improve management of the captive population of two-toed sloths. Zoo Biol 30:623-635, 2011. © 2010 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2011
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49. Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes

Author

Hoekstra, Hopi, Weber, Jesse N, and Steiner, Cynthia C

Subjects
evolutionary biology
Abstract

Little is known about the genetic basis of ecologically important morphological variation such as the diverse color patterns of mammals. Here we identify genetic changes contributing to an adaptive difference in color pattern between two subspecies of oldfield mice (Peromyscus polionotus). One mainland subspecies has a cryptic dark brown dorsal coat, while a younger beach-dwelling subspecies has a lighter coat produced by natural selection for camouflage on pale coastal sand dunes. Using genome-wide linkage mapping, we identified three chromosomal regions (two of major and one of minor effect) associated with differences in pigmentation traits. Two candidate genes, the melanocortin-1 receptor (Mc1r) and its antagonist, the Agouti signaling protein (Agouti), map to independent regions that together are responsible for most of the difference in pigmentation between subspecies. A derived mutation in the coding region of Mc1r, rather than change in its expression level, contributes to light pigmentation. Conversely, beach mice have a derived increase in Agouti mRNA expression but no changes in protein sequence. These two genes also interact epistatically: the phenotypic effects of Mc1r are visible only in genetic backgrounds containing the derived Agouti allele. These results demonstrate that cryptic coloration can be based largely on a few interacting genes of major effect., Organismic and Evolutionary Biology

Published
2007
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