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1. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Author

Warren, Wesley C, Harris, R Alan, Haukness, Marina, Fiddes, Ian T, Murali, Shwetha C, Fernandes, Jason, Dishuck, Philip C, Storer, Jessica M, Raveendran, Muthuswamy, Hillier, LaDeana W, Porubsky, David, Mao, Yafei, Gordon, David, Vollger, Mitchell R, Lewis, Alexandra P, Munson, Katherine M, DeVogelaere, Elizabeth, Armstrong, Joel, Diekhans, Mark, Walker, Jerilyn A, Tomlinson, Chad, Graves-Lindsay, Tina A, Kremitzki, Milinn, Salama, Sofie R, Audano, Peter A, Escalona, Merly, Maurer, Nicholas W, Antonacci, Francesca, Mercuri, Ludovica, Maggiolini, Flavia AM, Catacchio, Claudia Rita, Underwood, Jason G, O'Connor, David H, Sanders, Ashley D, Korbel, Jan O, Ferguson, Betsy, Kubisch, H Michael, Picker, Louis, Kalin, Ned H, Rosene, Douglas, Levine, Jon, Abbott, David H, Gray, Stanton B, Sanchez, Mar M, Kovacs-Balint, Zsofia A, Kemnitz, Joseph W, Thomasy, Sara M, Roberts, Jeffrey A, Kinnally, Erin L, Capitanio, John P, Skene, JH Pate, Platt, Michael, Cole, Shelley A, Green, Richard E, Ventura, Mario, Wiseman, Roger W, Paten, Benedict, Batzer, Mark A, Rogers, Jeffrey, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, HIV/AIDS, Biotechnology, Animals, Genetic Predisposition to Disease, Genetic Variation, Genome, Humans, Macaca mulatta, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Whole Genome Sequencing, General Science & Technology
Abstract

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

Published
2020

2. The comparative genomics and complex population history of Papio baboons.

Author

Rogers, Jeffrey, Raveendran, Muthuswamy, Harris, R, Mailund, Thomas, Leppälä, Kalle, Athanasiadis, Georgios, Schierup, Mikkel, Cheng, Jade, Munch, Kasper, Walker, Jerilyn, Konkel, Miriam, Jordan, Vallmer, Steely, Cody, Beckstrom, Thomas, Bergey, Christina, Burrell, Andrew, Schrempf, Dominik, Noll, Angela, Kothe, Maximillian, Kopp, Gisela, Liu, Yue, Murali, Shwetha, Billis, Konstantinos, Martin, Fergal, Muffato, Matthieu, Cox, Laura, Else, James, Disotell, Todd, Muzny, Donna, Phillips-Conroy, Jane, Aken, Bronwen, Eichler, Evan, Marques-Bonet, Tomas, Kosiol, Carolin, Batzer, Mark, Hahn, Matthew, Tung, Jenny, Zinner, Dietmar, Roos, Christian, Jolly, Clifford, Gibbs, Richard, and Worley, Kim

Subjects
Animals, Base Sequence, Biological Evolution, Female, Gene Flow, Genomics, Haplotypes, Humans, Hybridization, Genetic, Male, Papio, Phylogeny, Polymorphism, Genetic, Whole Genome Sequencing
Abstract

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

Published
2019

3. A high-quality bonobo genome refines the analysis of hominid evolution

Author

Mao, Yafei, Catacchio, Claudia R., Hillier, LaDeana W., Porubsky, David, Li, Ruiyang, Sulovari, Arvis, Fernandes, Jason D., Montinaro, Francesco, Gordon, David S., Storer, Jessica M., Haukness, Marina, Fiddes, Ian T., Murali, Shwetha Canchi, Dishuck, Philip C., Hsieh, PingHsun, Harvey, William T., Audano, Peter A., Mercuri, Ludovica, Piccolo, Ilaria, Antonacci, Francesca, Munson, Katherine M., Lewis, Alexandra P., Baker, Carl, Underwood, Jason G., Hoekzema, Kendra, Huang, Tzu-Hsueh, Sorensen, Melanie, Walker, Jerilyn A., Hoffman, Jinna, Thibaud-Nissen, Françoise, Salama, Sofie R., Pang, Andy W. C., Lee, Joyce, Hastie, Alex R., Paten, Benedict, Batzer, Mark A., Diekhans, Mark, Ventura, Mario, and Eichler, Evan E.

Published
2021
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5. An integrated map of structural variation in 2,504 human genomes.

Author

Sudmant, Peter H, Rausch, Tobias, Gardner, Eugene J, Handsaker, Robert E, Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Fritz, Markus Hsi-Yang, Konkel, Miriam K, Malhotra, Ankit, Stütz, Adrian M, Shi, Xinghua, Casale, Francesco Paolo, Chen, Jieming, Hormozdiari, Fereydoun, Dayama, Gargi, Chen, Ken, Malig, Maika, Chaisson, Mark JP, Walter, Klaudia, Meiers, Sascha, Kashin, Seva, Garrison, Erik, Auton, Adam, Lam, Hugo YK, Mu, Xinmeng Jasmine, Alkan, Can, Antaki, Danny, Bae, Taejeong, Cerveira, Eliza, Chines, Peter, Chong, Zechen, Clarke, Laura, Dal, Elif, Ding, Li, Emery, Sarah, Fan, Xian, Gujral, Madhusudan, Kahveci, Fatma, Kidd, Jeffrey M, Kong, Yu, Lameijer, Eric-Wubbo, McCarthy, Shane, Flicek, Paul, Gibbs, Richard A, Marth, Gabor, Mason, Christopher E, Menelaou, Androniki, Muzny, Donna M, Nelson, Bradley J, Noor, Amina, Parrish, Nicholas F, Pendleton, Matthew, Quitadamo, Andrew, Raeder, Benjamin, Schadt, Eric E, Romanovitch, Mallory, Schlattl, Andreas, Sebra, Robert, Shabalin, Andrey A, Untergasser, Andreas, Walker, Jerilyn A, Wang, Min, Yu, Fuli, Zhang, Chengsheng, Zhang, Jing, Zheng-Bradley, Xiangqun, Zhou, Wanding, Zichner, Thomas, Sebat, Jonathan, Batzer, Mark A, McCarroll, Steven A, 1000 Genomes Project Consortium, Mills, Ryan E, Gerstein, Mark B, Bashir, Ali, Stegle, Oliver, Devine, Scott E, Lee, Charles, Eichler, Evan E, and Korbel, Jan O

Subjects
Genomes Project Consortium, Humans, Genetic Predisposition to Disease, Physical Chromosome Mapping, Sequence Analysis, DNA, Genetics, Medical, Genetics, Population, Genomics, Sequence Deletion, Amino Acid Sequence, Genotype, Haplotypes, Homozygote, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome, Human, Molecular Sequence Data, Genetic Variation, Genome-Wide Association Study, Mutation Rate, Sequence Analysis, DNA, Genetics, Medical, Population, Polymorphism, Single Nucleotide, Genome, Human, General Science & Technology
Abstract

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Published
2015

6. 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
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7. Rates and patterns of great ape retrotransposition

Author

Hormozdiari, Fereydoun, Konkel, Miriam K, Prado-Martinez, Javier, Chiatante, Giorgia, Herraez, Irene Hernando, Walker, Jerilyn A, Nelson, Benjamin, Alkan, Can, Sudmant, Peter H, Huddleston, John, Catacchio, Claudia R, Ko, Arthur, Malig, Maika, Baker, Carl, Project, Great Ape Genome, Marques-Bonet, Tomas, Ventura, Mario, Batzer, Mark A, and Eichler, Evan E

Subjects
Genetics, Human Genome, Alu Elements, Animals, Cluster Analysis, DNA Primers, Genetic Variation, Genome, Genomics, Hominidae, Humans, Likelihood Functions, Long Interspersed Nucleotide Elements, Phylogeny, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Principal Component Analysis, Species Specificity, genomics, genetic diversity, structural variation, retrotransposon, Great Ape Genome Project
Abstract

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.

Published
2013

8. Orangutan Alu Quiescence Reveals Possible Source Element: Support for Ancient Backseat Drivers

Author

Walker, Jerilyn A, Konkel, Miriam K, Ullmer, Brygg, Monceaux, Christopher P, Ryder, Oliver A, Hubley, Robert, Smit, Arian FA, and Batzer, Mark A

Abstract

Abstract Background Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. Results Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. Conclusions This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.

Published
2012

9. Mapping copy number variation by population-scale genome sequencing.

Author

Mills, Ryan, Walter, Klaudia, Stewart, Chip, Handsaker, Robert, Chen, Ken, Alkan, Can, Abyzov, Alexej, Yoon, Seungtai, Ye, Kai, Cheetham, R, Chinwalla, Asif, Conrad, Donald, Fu, Yutao, Grubert, Fabian, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Iakoucheva, Lilia, Iqbal, Zamin, Kang, Shuli, Kidd, Jeffrey, Konkel, Miriam, Korn, Joshua, Khurana, Ekta, Kural, Deniz, Lam, Hugo, Leng, Jing, Li, Ruiqiang, Li, Yingrui, Lin, Chang-Yun, Luo, Ruibang, Mu, Xinmeng, Nemesh, James, Peckham, Heather, Rausch, Tobias, Scally, Aylwyn, Shi, Xinghua, Stromberg, Michael, Stütz, Adrian, Urban, Alexander, Walker, Jerilyn, Wu, Jiantao, Zhang, Yujun, Zhang, Zhengdong, Batzer, Mark, Ding, Li, Marth, Gabor, McVean, Gil, Sebat, Jonathan, Snyder, Michael, Wang, Jun, Ye, Kenny, Eichler, Evan, Gerstein, Mark, Hurles, Matthew, Lee, Charles, McCarroll, Steven, and Korbel, Jan

Subjects
DNA Copy Number Variations, Gene Duplication, Genetic Predisposition to Disease, Genetics, Population, Genome, Human, Genomics, Genotype, Humans, Mutagenesis, Insertional, Reproducibility of Results, Sequence Analysis, DNA, Sequence Deletion
Abstract

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

Published
2011

11. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author

Sørensen, Erik F., primary, Harris, R. Alan, additional, Zhang, Liye, additional, Raveendran, Muthuswamy, additional, Kuderna, Lukas F. K., additional, Walker, Jerilyn A., additional, Storer, Jessica M., additional, Kuhlwilm, Martin, additional, Fontsere, Claudia, additional, Seshadri, Lakshmi, additional, Bergey, Christina M., additional, Burrell, Andrew S., additional, Bergman, Juraj, additional, Phillips-Conroy, Jane E., additional, Shiferaw, Fekadu, additional, Chiou, Kenneth L., additional, Chuma, Idrissa S., additional, Keyyu, Julius D., additional, Fischer, Julia, additional, Gingras, Marie-Claude, additional, Salvi, Sejal, additional, Doddapaneni, Harshavardhan, additional, Schierup, Mikkel H., additional, Batzer, Mark A., additional, Jolly, Clifford J., additional, Knauf, Sascha, additional, Zinner, Dietmar, additional, Farh, Kyle K.-H., additional, Marques-Bonet, Tomas, additional, Munch, Kasper, additional, Roos, Christian, additional, and Rogers, Jeffrey, additional

Published
2023
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12. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author

Fundación la Caixa, Vienna Science and Technology Fund, German Research Foundation, Novo Nordisk Foundation, Baylor College of Medicine, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F. K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie-Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel Heide, Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle Kai-How, Marqués-Bonet, Tomàs, Munch, Kasper, Roos, Christian, Rogers, Jeffrey, Fundación la Caixa, Vienna Science and Technology Fund, German Research Foundation, Novo Nordisk Foundation, Baylor College of Medicine, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F. K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie-Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel Heide, Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle Kai-How, Marqués-Bonet, Tomàs, Munch, Kasper, Roos, Christian, and Rogers, Jeffrey

Abstract

[INTRODUCTION] As a widespread but comparatively young clade of six parapatric species, the baboons (Papio sp.) exemplify a frequently observed pattern of mammalian diversity. In particular, they provide analogs for the population structure of the multibranched prehuman lineage that occupied a similar geographic range before the hegemony of “modern” humans, Homo sapiens. Despite phenotypic and genetic differences, interspecies hybridization has been described between baboons at several locations, and population relationships based on mitochondrial DNA (mtDNA) do not correspond with relationships based on phenotype. These previous studies captured the broad outlines of baboon population genetic structure and evolutionary history but necessarily used data that were limited in genomic and geographical coverage and therefore could not adequately document inter- and intrapopulation variation. In this study, we analyzed whole-genome sequences of 225 baboons representing all six species and 19 geographic sites, with 18 local populations represented by multiple individuals., [RATIONALE] Recent studies have identified several mammalian species groups in which genetically distinct lineages have hybridized to generate complex reticulate phylogenies. Baboons provide a valuable context for studying processes generating such population and phylogenetic complexity because extant parapatric species form hybrid zones in several regions of Africa, allowing for direct observation of ongoing introgression. Furthermore, prior studies of nuclear and mtDNA and phenotypic diversity have demonstrated gene flow among differentiated lineages but were unable to develop the detailed picture of process and history that is now possible using whole-genome sequences and modern computational methods. To address these questions, we designed a study that would provide a more fine-grained picture of recent and ancient genetic reticulation by comparing phenotypes and autosomal, X and Y chromosomal, and mtDNA sequences, along with polymorphic insertions of repetitive elements across multiple baboon populations., [RESULTS] Using deep whole-genome sequence data from 225 baboons representing multiple populations, we identified several previously unknown geographic sites of gene flow between genetically distinct populations. We report that yellow baboons (P. cynocephalus) from western Tanzania are the first nonhuman primate found to have received genetic input from three distinct lineages. We compared the ancestry shared among individuals, estimated separately from the X chromosome and autosomes, to distinguish shared ancestry due to ancestral population relationships from coancestry as a result of recent male-biased immigration and gene flow. This reveals directionality and sex bias of recent gene flow in several locations. Analyses of population differences within species quantified different degrees of interspecies introgression among populations with an essentially identical phenotype., [CONCLUSION] The population genetic structure and history of introgression among baboon lineages are even more complex than predicted from observed phenotypic diversity and prior studies of limited genetic data. Single populations can carry genetic contributions from more than two ancestral sources. Populations that appear homogeneous on the basis of observable phenotype can display different levels of interspecies introgression. The evolutionary dynamics and current structure of baboon population diversity indicate that other mammals displaying differentiated and geographically separate species may also have more-complex histories than anticipated. This may also be true for the morphologically defined hominin taxa from the past 4 million years.

Published
2023

13. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author

Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F.K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel H., Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle K.H., Marques-Bonet, Tomas, Munch, Kasper, Roos, Christian, and Rogers, Jeffrey

Subjects
Article
Abstract

Baboons (genusPapio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.One-Sentence SummaryGenomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.

Published
2023
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20. Rates and patterns of great ape retrotransposition

Author

Great Ape Genome Project, Hormozdiari, Fereydoun, Konkel, Miriam K., Prado-Martinez, Javier, Chiatante, Giorgia, Herraez, Irene Hernando, Walker, Jerilyn A., Nelson, Benjamin, Alkan, Can, Sudmant, Peter H., Huddleston, John, Catacchio, Claudia R., Ko, Arthur, Malig, Maika, Baker, Carl, Marques-Bonet, Tomas, Ventura, Mario, Batzer, Mark A., and Eichler, Evan E.

Published
2013

21. Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics

Author

National Institutes of Health (US), Storer, Jessica M., Walker, Jerilyn A., Rockwell, Catherine E., Mores, Grayce, Beckstrom, Thomas O., Orkin, Joseph D., Melin, Amanda D., Phillips, Kimberley A., Roos, Christian, Batzer, Mark A., National Institutes of Health (US), Storer, Jessica M., Walker, Jerilyn A., Rockwell, Catherine E., Mores, Grayce, Beckstrom, Thomas O., Orkin, Joseph D., Melin, Amanda D., Phillips, Kimberley A., Roos, Christian, and Batzer, Mark A.

Abstract

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.

Published
2022

23. Gibbon genome and the fast karyotype evolution of small apes

Author

Carbone, Lucia, Alan Harris, R., Gnerre, Sante, Veeramah, Krishna R., Lorente-Galdos, Belen, Huddleston, John, Meyer, Thomas J., Herrero, Javier, Roos, Christian, Aken, Bronwen, Anaclerio, Fabio, Archidiacono, Nicoletta, Baker, Carl, Barrell, Daniel, Batzer, Mark A., Beal, Kathryn, Blancher, Antoine, Bohrson, Craig L., Brameier, Markus, Campbell, Michael S., Capozzi, Oronzo, Casola, Claudio, Chiatante, Giorgia, Cree, Andrew, Damert, Annette, de Jong, Pieter J., Dumas, Laura, Fernandez-Callejo, Marcos, Flicek, Paul, Fuchs, Nina V., Gut, Ivo, Gut, Marta, Hahn, Matthew W., Hernandez-Rodriguez, Jessica, Hillier, LaDeana W., Hubley, Robert, Ianc, Bianca, Izsvák, Zsuzsanna, Jablonski, Nina G., Johnstone, Laurel M., Karimpour-Fard, Anis, Konkel, Miriam K., Kostka, Dennis, Lazar, Nathan H., Lee, Sandra L., Lewis, Lora R., Liu, Yue, Locke, Devin P., Mallick, Swapan, Mendez, Fernando L., Muffato, Matthieu, Nazareth, Lynne V., Nevonen, Kimberly A., O’Bleness, Majesta, Ochis, Cornelia, Odom, Duncan T., Pollard, Katherine S., Quilez, Javier, Reich, David, Rocchi, Mariano, Schumann, Gerald G., Searle, Stephen, Sikela, James M., Skollar, Gabriella, Smit, Arian, Sonmez, Kemal, Hallers, Boudewijn ten, Terhune, Elizabeth, Thomas, Gregg W. C., Ullmer, Brygg, Ventura, Mario, Walker, Jerilyn A., Wall, Jeffrey D., Walter, Lutz, Ward, Michelle C., Wheelan, Sarah J., Whelan, Christopher W., White, Simon, Wilhelm, Larry J., Woerner, August E., Yandell, Mark, Zhu, Baoli, Hammer, Michael F., Marques-Bonet, Tomas, Eichler, Evan E., Fulton, Lucinda, Fronick, Catrina, Muzny, Donna M., Warren, Wesley C., Worley, Kim C., Rogers, Jeffrey, Wilson, Richard K., and Gibbs, Richard A.

Published
2014
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24. Genome-wide analysis of the human Alu Yb-lineage

Author

Carter Anthony B, Salem Abdel-Halim, Hedges Dale J, Keegan Catherine, Kimball Beth, Walker Jerilyn A, Watkins W, Jorde Lynn B, and Batzer Mark A

Subjects
mobile elements, SINEs, Medicine, Genetics, QH426-470
Abstract

Abstract The Alu Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for Alu Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb Alu subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the Alu Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage Alu elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx Alu family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that Alu Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the Alu Yb elements will be useful in a wide range of genetic analyses.

Published
2004
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25. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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26. Improved gnss-r altimetry methods: Theory and experimental demonstration using airborne dual frequency data from the microwave interferometric reflectometer (mir)

Author

Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Cervelló i Nogues, Oriol, Muñoz-Martín, Joan Francesc, Park, Hyuk, Camps, Adriano, Onrubia, Raul, Pascual, Daniel, Rüdiger, Christoph, Walker, Jerilyn A., Monerris, A., Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Cervelló i Nogues, Oriol, Muñoz-Martín, Joan Francesc, Park, Hyuk, Camps, Adriano, Onrubia, Raul, Pascual, Daniel, Rüdiger, Christoph, Walker, Jerilyn A., and Monerris, A.

Abstract

Altimetric performance of Global Navigation Satellite System-Reflectometry (GNSS-R) instruments depends on receiver’s bandwidth and signal-to-noise ratio (SNR). The altimetric delay is usually computed from the time difference between the peak of the direct signal waveform and the maximum of the derivative of the reflected signal waveform. Dual-frequency data gathered by the airborne Microwave Interferometric Reflectometer (MIR) in the Bass Strait, between Australia and Tasmania, suggest that this approach is only valid for flat surfaces and large bandwidth receivers. This work analyses different methods to compute the altimetric observables using GNSS-R. A proposed novel method, the Peak-to-Minimum of the 3rd Derivative (P-Min3D) for narrow-band codes (e.g., L1 C/A), and the Peak-to-Half Power (P-HP) for large bandwidth codes (e.g., L5 or E5a codes) show improved performance when using real data. Both methods are also compared to the Peak-to-Peak (P-P) and Peak-to-Maximum of the 1st Derivative (P-Max1D) methods. The key difference between these methods is the determination of the delay position in the reflected signal waveform in order to compute the altimetric observable. Airborne experimental results comparing the different methods, bands and GNSS-R processing techniques show that centimeter level accuracy can be achieved.

Published
2021

27. 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, Valle, Giuliano Della, 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
2011
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28. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Author

Mikkelsen, Tarjei S., Wakefield, Matthew J., Aken, Bronwen, Amemiya, Chris T., Chang, Jean L., Duke, Shannon, Garber, Manuel, Gentles, Andrew J., Goodstadt, Leo, Heger, Andreas, Jurka, Jerzy, Kamal, Michael, Mauceli, Evan, Searle, Stephen M. J., Sharpe, Ted, Baker, Michelle L., Batzer, Mark A., Benos, Panayiotis V., Belov, Katherine, Clamp, Michele, Cook, April, Cuff, James, Das, Radhika, Davidow, Lance, Deakin, Janine E., Fazzari, Melissa J., Glass, Jacob L., Grabherr, Manfred, Greally, John M., Gu, Wanjun, Hore, Timothy A., Huttley, Gavin A., Kleber, Michael, Jirtle, Randy L., Koina, Edda, Lee, Jeannie T., Mahony, Shaun, Marra, Marco A., Miller, Robert D., Nicholls, Robert D., Oda, Mayumi, Papenfuss, Anthony T., Parra, Zuly E., Pollock, David D., Ray, David A., Schein, Jacqueline E., Speed, Terence P., Thompson, Katherine, VandeBerg, John L., Wade, Claire M., Walker, Jerilyn A., Waters, Paul D., Webber, Caleb, Weidman, Jennifer R., Xie, Xiaohui, Zody, Michael C., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Acer, St Christophe, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Husby, M. Erii, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Jaffe, David B., Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Gnerre, Sante, MacCallum, Iain, Graves, Jennifer A. Marshall, Ponting, Chris P., Breen, Matthew, Samollow, Paul B., Lander, Eric S., and Lindblad-Toh, Kerstin

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Tarjei S. Mikkelsen (corresponding author) [1, 2]; Matthew J. Wakefield [3]; Bronwen Aken [4]; Chris T. Amemiya [5]; Jean L. Chang [1]; Shannon Duke [6]; Manuel Garber [1]; Andrew [...]

Published
2007
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31. Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus / Sapajus Genomics.

Author

Storer, Jessica M., Walker, Jerilyn A., Rockwell, Catherine E., Mores, Grayce, Beckstrom, Thomas O., Orkin, Joseph D., Melin, Amanda D., Phillips, Kimberley A., Roos, Christian, and Batzer, Mark A.

Subjects
*CAPUCHIN monkeys, *GENOMICS, *RETROTRANSPOSONS, *MONKEYS, *OLIGONUCLEOTIDES
Abstract

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships. [ABSTRACT FROM AUTHOR]

Published
2022
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32. An integrated map of genetic variation from 1,092 human genomes

Author

McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Clark, Andrew G., Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariyal, Ridhi, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Sudbrak, Herwig, Ralf, Shriver, Mark D., Bustamante, Carlos D., Byrnes, Jake K., De La Vega, Francisco M., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., James Kent, W., Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Min Kang, Hyun, Anderson, Paul, Angius, Andrea, Bigham, Abigail, Blackwell, Tom, Busonero, Fabio, Cucca, Francesco, Fuchsberger, Christian, Jones, Chris, Jun, Goo, Li, Yun, Lyons, Robert, Maschio, Andrea, Porcu, Eleonora, Reinier, Fred, Sanna, Serena, Schlessinger, David, Sidore, Carlo, Tan, Adrian, Kate Trost, Mary, Awadalla, Philip, Hodgkinson, Alan, Lunter, Gerton, McVean, Gil A., Marchini, Jonathan L., Myers, Simon, Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Eichler, Evan E., Browning, Brian L., Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Hurles, Matthew E., Tyler-Smith, Chris, Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Li, Heng, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Gerstein, Mark B., Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Jin, Mike, Khurana, Ekta, Jasmine Mu, Xinmeng, Sisu, Cristina, Lee, Charles, McCarroll, Steven A., Degenhardt, Jeremiah, Korbel, Jan O., Stütz, Adrian M., Church, Deanna, Michaelson, Jacob J., Eichler, Evan E., Hurles, Matthew E., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, DePristo, Mark A., Min Kang, Hyun, Mardis, Elaine R., Yu, Fuli, Michelson, Leslie P., Tyler-Smith, Chris, Frankish, Adam, Harrow, Jennifer, Fowler, Gerald, Hale, Walker, Kalra, Divya, Flicek, Paul, Clarke, Laura, Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Vaughan, Brendan, Sherry, Stephen T., Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, OʼSullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Chakravarti, Aravinda, Knoppers, Bartha M., Barnes, Kathleen C., Beiswanger, Christine, Burchard, Esteban G., Bustamante, Carlos D., Cai, Hongyu, Cao, Hongzhi, Durbin, Richard M., Gharani, Neda, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Reich, David, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H., Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Ruiz-Linares, Andres, Zhi Ming, Cai, Yang, Gao, Jia You, Chu, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Oleksyk, Taras K., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Duncanson, Audrey, Dunn, Michael, Guyer, Mark S., Peterson, Jane L., Abecasis, Goncalo R., and Auton, Adam

Published
2012
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33. A map of human genome variation from population-scale sequencing

Author

Durbin, Richard M., Altshuler, David L., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Knoppers, Bartha M., Lander, Eric S., Lehrach, Hans, Mardis, Elaine R., McVean, Gil A., Nickerson, Debbie A., Peltonen, Leena, Schafer, Alan J., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Gibbs, Richard A., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Wang, Jun, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Lander, Eric S., Altshuler, David L., Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Gabriel, Stacey B., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Bentley, David R., Gormley, Niall, Humphray, Sean, Kingsbury, Zoya, Koko-Gonzales, Paula, Stone, Jennifer, McKernan, Kevin J., Costa, Gina L., Ichikawa, Jeffry K., Lee, Clarence C., Sudbrak, Ralf, Lehrach, Hans, Borodina, Tatiana A., Dahl, Andreas, Davydov, Alexey N., Marquardt, Peter, Mertes, Florian, Nietfeld, Wilfiried, Rosenstiel, Philip, Schreiber, Stefan, Soldatov, Aleksey V., Timmermann, Bernd, Tolzmann, Marius, Egholm, Michael, Affourtit, Jason, Ashworth, Dana, Attiya, Said, Bachorski, Melissa, Buglione, Eli, Burke, Adam, Caprio, Amanda, Celone, Christopher, Clark, Shauna, Conners, David, Desany, Brian, Gu, Lisa, Guccione, Lorri, Kao, Kalvin, Kebbel, Andrew, Knowlton, Jennifer, Labrecque, Matthew, McDade, Louise, Mealmaker, Craig, Minderman, Melissa, Nawrocki, Anne, Niazi, Faheem, Pareja, Kristen, Ramenani, Ravi, Riches, David, Song, Wanmin, Turcotte, Cynthia, Wang, Shally, Mardis, Elaine R., Wilson, Richard K., Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, Durbin, Richard M., Burton, John, Carter, David M., Churcher, Carol, Coffey, Alison, Cox, Anthony, Palotie, Aarno, Quail, Michael, Skelly, Tom, Stalker, James, Swerdlow, Harold P., Turner, Daniel, De Witte, Anniek, Giles, Shane, Bainbridge, Matthew, Challis, Danny, Sabo, Aniko, Yu, Fuli, Yu, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Marth, Gabor T., Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Quinlan, Aaron R., Stewart, Chip, Stromberg, Michael P., Ward, Alistair N., Wu, Jiantao, Lee, Charles, Mills, Ryan E., Shi, Xinghua, Daly, Mark J., DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon R., Handsaker, Robert E., Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Korn, Joshua M., Li, Heng, Maguire, Jared R., McCarroll, Steven A., McKenna, Aaron, Nemesh, James C., Philippakis, Anthony A., Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis C., Schaffner, Stephen F., Shlyakhter, Ilya A., Cooper, David N., Ball, Edward V., Mort, Matthew, Phillips, Andrew D., Stenson, Peter D., Sebat, Jonathan, Makarov, Vladimir, Ye, Kenny, Yoon, Seungtai C., Bustamante, Carlos D., Clark, Andrew G., Boyko, Adam, Degenhardt, Jeremiah, Gravel, Simon, Gutenkunst, Ryan N., Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, Flicek, Paul, Cunningham, Fiona, Herrero, Javier, Keenen, Stephen, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Smith, Richard E., Zalunin, Vadim, Zheng-Bradley, Xiangqun, Korbel, Jan O., Stütz, Adrian M., Humphray, Sean, Bauer, Markus, Cheetham, Keira R., Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, De La Vega, Francisco M., Fu, Yutao, Hyland, Fiona C. L., Manning, Jonathan M., McLaughlin, Stephen F., Peckham, Heather E., Sakarya, Onur, Sun, Yongming A., Tsung, Eric F., Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Herwig, Ralf, Parkhomchuk, Dimitri V., Sherry, Stephen T., Agarwala, Richa, Khouri, Hoda M., Morgulis, Aleksandr O., Paschall, Justin E., Phan, Lon D., Rotmistrovsky, Kirill E., Sanders, Robert D., Shumway, Martin F., Xiao, Chunlin, McVean, Gil A., Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, Desany, Brian, Knight, James, Winer, Roger, Craig, David W., Beckstrom-Sternberg, Steve M., Christoforides, Alexis, Kurdoglu, Ahmet A., Pearson, John V., Sinari, Shripad A., Tembe, Waibhav D., Haussler, David, Hinrichs, Angie S., Katzman, Sol J., Kern, Andrew, Kuhn, Robert M., Przeworski, Molly, Hernandez, Ryan D., Howie, Bryan, Kelley, Joanna L., Cord Melton, S., Abecasis, Gonçalo R., Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Min Kang, Hyun, Lathrop, Mark, Liang, Liming, Moffatt, Miriam F., Scheet, Paul, Sidore, Carlo, Snyder, Matthew, Zhan, Xiaowei, Zöllner, Sebastian, Awadalla, Philip, Casals, Ferran, Idaghdour, Youssef, Keebler, John, Stone, Eric A., Zilversmit, Martine, Jorde, Lynn, Xing, Jinchuan, Eichler, Evan E., Aksay, Gozde, Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, Cenk S., Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Koboldt, Daniel C., McLellan, Mike D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Albers, Cornelis A., Ayub, Qasim, Balasubramaniam, Senduran, Barrett, Jeffrey C., Chen, Yuan, Conrad, Donald F., Danecek, Petr, Dermitzakis, Emmanouil T., Hu, Min, Huang, Ni, Hurles, Matt E., Jin, Hanjun, Jostins, Luke, Keane, Thomas M., Quang Le, Si, Lindsay, Sarah, Long, Quan, MacArthur, Daniel G., Montgomery, Stephen B., Parts, Leopold, Tyler-Smith, Chris, Walter, Klaudia, Zhang, Yujun, Gerstein, Mark B., Snyder, Michael, Abyzov, Alexej, Balasubramanian, Suganthi, Bjornson, Robert, Du, Jiang, Grubert, Fabian, Habegger, Lukas, Haraksingh, Rajini, Jee, Justin, Khurana, Ekta, Lam, Hugo Y. K., Leng, Jing, Jasmine Mu, Xinmeng, Urban, Alexander E., Zhang, Zhengdong, Lee, Charles, McCarroll, Steven A., DePristo, Mark A., Korbel, Jan O., De La Vega, Francisco M., Blackwell, Tom, Eichler, Evan E., Kidd, Jeffrey M., Hurles, Matt E., Gibbs, Richard A., Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Marth, Gabor T., Wilkinson, Jane, Flicek, Paul, Sherry, Stephen T., Abecasis, Gonçalo R., Mardis, Elaine R., Coffey, Allison, Scott, Carol, Gerstein, Mark B., Chakravarti, Aravinda, Knoppers, Bartha M., Bustamante, Carlos D., Gharani, Neda, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Abdallah, Assya, Juenger, Christopher R., Clemm, Nicholas C., Duncanson, Audrey, Green, Eric D., Guyer, Mark S., and Peterson, Jane L.

Published
2010
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34. HRAS1 and LASS1 with APOE are associated with human longevity and healthy aging

Author

Jazwinski, Michal S., Kim, Sangkyu, Dai, Jianliang, Li, Li, Bi, Xiuhua, Jiang, James C., Arnold, Jonathan, Batzer, Mark A., Walker, Jerilyn A., Welsh, David A., Lefante, Christina M., Volaufova, Julia, Myers, Leann, Su, Joseph L., Hausman, Dorothy B., Miceli, Michael V., Ravussin, Eric, Poon, Leonard W., Cherry, Katie E., and Welsch, Michael A.

Published
2010
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35. The genome of a songbird

Author

Warren, Wesley C., Clayton, David F., Ellegren, Hans, Arnold, Arthur P., Hillier, LaDeana W., Künstner, Axel, Searle, Steve, White, Simon, Vilella, Albert J., Fairley, Susan, Heger, Andreas, Kong, Lesheng, Ponting, Chris P., Jarvis, Erich D., Mello, Claudio V., Minx, Pat, Lovell, Peter, Velho, Tarciso A. F., Ferris, Margaret, Balakrishnan, Christopher N., Sinha, Saurabh, Blatti, Charles, London, Sarah E., Li, Yun, Lin, Ya-Chi, George, Julia, Sweedler, Jonathan, Southey, Bruce, Gunaratne, Preethi, Watson, Michael, Nam, Kiwoong, Backström, Niclas, Smeds, Linnea, Nabholz, Benoit, Itoh, Yuichiro, Whitney, Osceola, Pfenning, Andreas R., Howard, Jason, Völker, Martin, Skinner, Bejamin M., Griffin, Darren K., Ye, Liang, McLaren, William M., Flicek, Paul, Quesada, Victor, Velasco, Gloria, Lopez-Otin, Carlos, Puente, Xose S., Olender, Tsviya, Lancet, Doron, Smit, Arian F. A., Hubley, Robert, Konkel, Miriam K., Walker, Jerilyn A., Batzer, Mark A., Gu, Wanjun, Pollock, David D., Chen, Lin, Cheng, Ze, Eichler, Evan E., Stapley, Jessica, Slate, Jon, Ekblom, Robert, Birkhead, Tim, Burke, Terry, Burt, David, Scharff, Constance, Adam, Iris, Richard, Hugues, Sultan, Marc, Soldatov, Alexey, Lehrach, Hans, Edwards, Scott V., Yang, Shiaw-Pyng, Li, XiaoChing, Graves, Tina, Fulton, Lucinda, Nelson, Joanne, Chinwalla, Asif, Hou, Shunfeng, Mardis, Elaine R., and Wilson, Richard K.

Published
2010
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37. Papio Baboon Species Indicative Alu Elements

Author

Walker, Jerilyn A., Jordan, Vallmer E., Steely, Cody J., Beckstrom, Thomas O., McDaniel, Cullen L., St Romain, Corey P., Bennett, Emily C., Robichaux, Arianna, Clement, Brooke N., Konkel, Miriam K., Baboon Genome Analysis Consortium, Marquès i Bonet, Tomàs, 1975, and Batzer, Mark A.

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Genotype, population genomics, Population, Alu element, Evolutionary biology, DNA, Mitochondrial, 010603 evolutionary biology, 01 natural sciences, Identity by descent, Population genomics, Sexual Behavior, Animal, 03 medical and health sciences, Gene Frequency, Alu Elements, Phylogenetics, biology.animal, Genetics, Animals, Retrotransposon, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, Phylogenetic tree, biology, retrotransposon, evolutionary biology, Genetic Variation, Pedigree, 030104 developmental biology, Genetic marker, Female, Papio, Research Article, Baboon
Abstract

The genus of Papio (baboon) has six recognized species separated into Northern and Southern clades, each comprised of three species distributed across the African continent. Geographic origin and phenotypic variants such as coat color and body size have commonly been used to identify different species. The existence of multiple hybrid zones, both ancient and current, have complicated efforts to characterize the phylogeny of Papio baboons. More recently, mitochondrial DNA (mtDNA) and Y-chromosome genetic markers have been utilized for species identification with particular focus on the hybrid zones. Alu elements accumulate in a random manner and are a novel source of identical by descent variation with known ancestral states for inferring population genetic and phylogenetic relationships. As part of the Baboon Genome Analysis Consortium, we assembled an Alu insertion polymorphism database of nearly 500 Papio-lineage specific insertions representing all six species and performed population structure and phylogenetic analyses. In this study, we have selected a subset of 48 species indicative Alu insertions and demonstrate their utility as genetic systems for the identification of baboon species within Papio. Individual elements from the panel are easy to genotype and can be used in a hierarchical fashion based on the original level of uncertainty. This Alu-48 panel should serve as a valuable tool during the maintenance of pedigree records in captive populations and assist in the forensic identification of fossils and potential hybrids in the wild.

Published
2017
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41. Misty (m) affects growth traits

Author

Truett, Gary E., Tempelman, Robert J., Walker, Jerilyn A., and Wilson, J. Krause

Subjects
Obesity -- Physiological aspects, Growth factors -- Genetic aspects, Mice as laboratory animals -- Genetic aspects, Biological sciences
Abstract

The effect of the gene coding for the misty coat color mutation, m, on the growth traits of mice in a population segregating this gene in the absence of the obesity mutation diabetes gene to determine if this gene will compound the measurement of traits affected by the obesity gene. Results reveal that m affects growth rates, body length, body weight and inguinal adipose tissue mass. The implications of these findings on obesity gene research are discussed.

Published
1998

43. Analysis of the Human Alu Ya-lineage

Author

Otieno, Anthony C., Carter, Anthony B., Hedges, Dale J., Walker, Jerilyn A., Ray, David A., Garber, Randall K., Anders, Bridget A., Stoilova, Nadica, Laborde, Meredith E., Fowlkes, Justin D., Huang, Cheney H., Perodeau, Benjamin, and Batzer, Mark A.

Published
2004
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44. The comparative genomics and complex population history of Papio baboons

Author

National Institutes of Health (US), Austrian Science Fund, Vienna Science and Technology Fund, Wellcome Trust, VEGA Agency (Slovakia), Fundación la Caixa, National Science Foundation (US), National Geographic Society, Leakey Foundation, Howard Hughes Medical Institute, Ministerio de Economía y Competitividad (España), European Commission, Rogers, Jeffrey, Raveendran, Muthuswamy, Alan Harris, R., Mailund, Thomas, Leppälä, Kalle, Athanasiadis, Georgios, Schierup, Mikkel Heide, Cheng, Jade, Munch, Kasper, Walker, Jerilyn A., Konkel, Miriam K., Jordan, Vallmer, Steely, Cody J., Beckstrom, Thomas O., Bergey, Christina, Burrell, Andrew, Schrempf, Dominik, Noll, Angela, Kothe, Maximillian, Kopp, Gisela H., Liu, Yue, Murali, Swetha, Billis, Konstantinos, Martin, Fergal J., Muffato, Matthieu, Cox, Laura, Else, James, Disotell, Todd, Muzny, Donna M., Phillips-Conroy, Jane, Aken, Bronwen, Eichler, Evan E., Marqués-Bonet, Tomàs, Kosiol, Carolin, Batzer, Mark A., Hahn, Matthiew W., Tung, Jenny, Zinner, Dietmar, Roos, Christian, Jolly, Clifford J., Gibbs, Richard A., Worley, Kim C., National Institutes of Health (US), Austrian Science Fund, Vienna Science and Technology Fund, Wellcome Trust, VEGA Agency (Slovakia), Fundación la Caixa, National Science Foundation (US), National Geographic Society, Leakey Foundation, Howard Hughes Medical Institute, Ministerio de Economía y Competitividad (España), European Commission, Rogers, Jeffrey, Raveendran, Muthuswamy, Alan Harris, R., Mailund, Thomas, Leppälä, Kalle, Athanasiadis, Georgios, Schierup, Mikkel Heide, Cheng, Jade, Munch, Kasper, Walker, Jerilyn A., Konkel, Miriam K., Jordan, Vallmer, Steely, Cody J., Beckstrom, Thomas O., Bergey, Christina, Burrell, Andrew, Schrempf, Dominik, Noll, Angela, Kothe, Maximillian, Kopp, Gisela H., Liu, Yue, Murali, Swetha, Billis, Konstantinos, Martin, Fergal J., Muffato, Matthieu, Cox, Laura, Else, James, Disotell, Todd, Muzny, Donna M., Phillips-Conroy, Jane, Aken, Bronwen, Eichler, Evan E., Marqués-Bonet, Tomàs, Kosiol, Carolin, Batzer, Mark A., Hahn, Matthiew W., Tung, Jenny, Zinner, Dietmar, Roos, Christian, Jolly, Clifford J., Gibbs, Richard A., and Worley, Kim C.

Abstract

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

Published
2019

45. Inference of human geographic origins using Alu insertion polymorphisms.

Author

Ray, David A., Walker, Jerilyn A., Hall, Ashley, Llewellyn, Barbara, Ballantyne, Jack, Christian, Allen T., Turteltaub, Kenneth, and Batzer, Mark A.

Subjects
Genomics -- Research, Genotype -- Research, Single nucleotide polymorphisms -- Research
Abstract

Abstract The inference of an individual's geographic ancestry or origin can be critical in narrowing the field of potential suspects in a criminal investigation. Most current technologies rely on single [...]

Published
2005

46. Codominant effects of the fatty (fa) gene during early development of obesity

Author

Truett, Gary E., Tempelman, Robert J., and Walker, Jerilyn A.

Subjects
Obesity -- Genetic aspects, Developmental genetics -- Analysis, Bioenergetics -- Analysis, Adipose tissues -- Research, Body weight -- Physiological aspects, Biological sciences
Abstract

Analysis of whether the expression of one copy of obesity fatty (fa) gene influences energy balance in rats reveals that the fa gene copy number linearly influences inguinal adipose pads and body weight at 7 days of age and linearly influences inguinal adipose pads, body and interscapular brown adipose tissue weights at 14 days of age. The recessive effects and codominant effects of the fa gene are detectable in the first and second weeks of growth, respectively.

Published
1995

50. Additional file 3: of A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

Author

Vallmer Jordan, Walker, Jerilyn, Beckstrom, Thomas, Steely, Cody, McDaniel, Cullen, Romain, Corey St., Worley, Kim, Phillips-Conroy, Jane, Jolly, Clifford, Rogers, Jeffrey, Konkel, Miriam, and Batzer, Mark

Abstract

An excel file containing a figure and table representing possible basal divergence model reconstructions generated using all six extant Papio species. A maximum of 31 rooted monophyletic models can be generated from such a genus comprised of six species. These models can be further organized into three distinct groups based on the number of species contained in the subsequent clades. Group I depicts the six different scenarios when one of the six species diverges prior to the other five. Group I-A) illustrates P. kindae diverging first, followed by B) P. ursinus first, then C-F) P. cynocephalus, P. papio, P. hamadryas, and P. anubis diverging first, respectively. Group II depicts the 15 different models when two of the six species diverge prior to the other four. All possible combinations of this scenario are illustrated in Group II A-O. Group III depicts the ten different models generated from a basal divergence that forms two clades each comprised of three species. All ten combinations are listed in Group III A-J. The values listed correspond to the 31 possible phylogenetic models displayed in Figure S1. For each model, the number of concordant insertions are provided in the third column; the number of discordant insertions can be found in the fourth column. The z-score determined for the number of discordant insertions is listed in the last column. The lowest z-score (indicating smallest proportion of discordant elements in group) is shown in bold font and indicates scenario III-A to be the most likely basal divergence model. (DOCX 61Â kb)

Published
2018
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