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1. Complexity of avian evolution revealed by family-level genomes

Author

Stiller, Josefin, Feng, Shaohong, Chowdhury, Al-Aabid, Rivas-González, Iker, Duchêne, David A., Fang, Qi, Deng, Yuan, Kozlov, Alexey, Stamatakis, Alexandros, Claramunt, Santiago, Nguyen, Jacqueline M. T., Ho, Simon Y. W., Faircloth, Brant C., Haag, Julia, Houde, Peter, Cracraft, Joel, Balaban, Metin, Mai, Uyen, Chen, Guangji, Gao, Rongsheng, Zhou, Chengran, Xie, Yulong, Huang, Zijian, Cao, Zhen, Yan, Zhi, Ogilvie, Huw A., Nakhleh, Luay, Lindow, Bent, Morel, Benoit, Fjeldså, Jon, Hosner, Peter A., da Fonseca, Rute R., Petersen, Bent, Tobias, Joseph A., Székely, Tamás, Kennedy, Jonathan David, Reeve, Andrew Hart, Liker, Andras, Stervander, Martin, Antunes, Agostinho, Tietze, Dieter Thomas, Bertelsen, Mads F., Lei, Fumin, Rahbek, Carsten, Graves, Gary R., Schierup, Mikkel H., Warnow, Tandy, Braun, Edward L., Gilbert, M. Thomas P., Jarvis, Erich D., Mirarab, Siavash, and Zhang, Guojie

Published
2024
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6. A region of suppressed recombination misleads neoavian phylogenomics

Author

Mirarab, Siavash, primary, Rivas-González, Iker, additional, Feng, Shaohong, additional, Stiller, Josefin, additional, Fang, Qi, additional, Mai, Uyen, additional, Hickey, Glenn, additional, Chen, Guangji, additional, Brajuka, Nadolina, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Wolf, Jochen B. W., additional, Howe, Kerstin, additional, Antunes, Agostinho, additional, Schierup, Mikkel H., additional, Paten, Benedict, additional, Jarvis, Erich D., additional, Zhang, Guojie, additional, and Braun, Edward L., additional

Published
2024
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8. A genomic history of Aboriginal Australia

Author

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

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

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

Published
2016

10. Strong selective sweeps associated with ampliconic regions in great ape X chromosomes

Author

Nam, Kiwoong, Munch, Kasper, Hobolth, Asger, Dutheil, Julien Y., Veeramah, Krishna, Woerner, August, Hammer, Michael F., Project, Great Ape Genome Diversity, Mailund, Thomas, and Schierup, Mikkel H.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes, and that a higher proportion of substitutions results from positive selection. Strikingly, the X exhibits several megabase long regions where diversity is reduced more than five fold. These regions overlap significantly among species, and have a higher singleton proportion, population differentiation, and nonsynonymous to synonymous substitution ratio. We rule out background selection and soft selective sweeps as explanations for these observations, and conclude that several strong selective sweeps have occurred independently in similar regions in several species. Since these regions are strongly associated with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution., Comment: This the resubmitted version, with supplementary

Published
2014

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

Author

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

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

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

Published
2015

13. Inference of Purifying and Positive Selection in Three Subspecies of Chimpanzees (Pan troglodytes) from Exome Sequencing

Author

Bataillon, Thomas, Duan, Jinjie, Hvilsom, Christina, Jin, Xin, Li, Yingrui, Skov, Laurits, Glemin, Sylvain, Munch, Kasper, Jiang, Tao, Qian, Yu, Hobolth, Asger, Wang, Jun, Mailund, Thomas, Siegismund, Hans R, and Schierup, Mikkel H

Subjects
Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Animals, Demography, Exome, Exons, Genetic Fitness, Genomics, Humans, INDEL Mutation, Pan troglodytes, Polymorphism, Single Nucleotide, Selection, Genetic, Sequence Analysis, DNA, effective size, fitness effect, mutation, selection, Biochemistry and Cell Biology, Evolutionary Biology, Developmental Biology
Abstract

We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called and genotyped for greater than 50% of exons at a mean coverage of 35× per individual. Central chimpanzees (Pan troglodytes troglodytes) are the most polymorphic (nucleotide diversity, θw = 0.0023 per site) followed by Eastern (P. t. schweinfurthii) chimpanzees (θw = 0.0016) and Western (P. t. verus) chimpanzees (θw = 0.0008). A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees. The striking contrast in X-linked versus autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection statistic exhibits a strong nonmonotonic relationship with the strength of purifying selection S, making it inappropriate for estimating S. We instead use counts in synonymous versus nonsynonymous frequency classes to infer the distribution of S coefficients acting on nonsynonymous mutations in each subspecies. The strength of purifying selection we infer is congruent with the differences in effective sizes of each subspecies: Central chimpanzees are undergoing the strongest purifying selection followed by Eastern and Western chimpanzees. Coding indels show stronger selection against indels changing the reading frame than observed in human populations.

Published
2015

14. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

Author

Li, Shengting, Besenbacher, Soren, Li, Yingrui, Kristiansen, Karsten, Grarup, Niels, Albrechtsen, Anders, Sparsø, Thomas, Korneliussen, Thorfinn, Hansen, Torben, Wang, Jun, Nielsen, Rasmus, Pedersen, Oluf, Bolund, Lars, and Schierup, Mikkel H

Subjects
Biological Sciences, Genetics, Human Genome, Diabetes, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Case-Control Studies, DNA, Mitochondrial, Denmark, Diabetes Mellitus, Exome, Gene Frequency, Genetic Association Studies, Genetic Variation, Genetics, Population, Genotype, Humans, Phylogeny, Polymorphism, Genetic, Quantitative Trait, Heritable, White People, diabetes, mtDNA, population history, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise the variation found in the mtDNA sequence in Danes and relate the variation to diabetes risk as well as to several blood phenotypes of the controls but find no significant associations. We report 2025 polymorphisms, of which 393 have not been reported previously. These 393 mutations are both very rare and estimated to be caused by very recent mutations but individuals with type 2 diabetes do not possess more of these variants. Population genetics analysis using Bayesian skyline plot shows a recent history of rapid population growth in the Danish population in accordance with the fact that >40% of variable sites are observed as singletons.

Published
2014

15. A high-coverage Neandertal genome from Vindija Cave in Croatia

Author

Prüfer, Kay, de Filippo, Cesare, Grote, Steffi, Mafessoni, Fabrizio, Korlević, Petra, Hajdinjak, Mateja, Vernot, Benjamin, Skov, Laurits, Hsieh, Pinghsun, Peyrégne, Stéphane, Reher, David, Hopfe, Charlotte, Nagel, Sarah, Maricic, Tomislav, Fu, Qiaomei, Theunert, Christoph, Rogers, Rebekah, Skoglund, Pontus, Chintalapati, Manjusha, Dannemann, Michael, Nelson, Bradley J., Key, Felix M., Rudan, Pavao, Kućan, Željko, Gušić, Ivan, Golovanova, Liubov V., Doronichev, Vladimir B., Patterson, Nick, Reich, David, Eichler, Evan E., Slatkin, Montgomery, Schierup, Mikkel H., Andrés, Aida M., Kelso, Janet, Meyer, Matthias, and Pääbo, Svante

Published
2017

16. Great ape genetic diversity and population history.

Author

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

Subjects
Animals, Animals, Wild, Animals, Zoo, Hominidae, Gorilla gorilla, Humans, Pan paniscus, Pan troglodytes, Inbreeding, Genetics, Population, Population Density, Evolution, Molecular, Phylogeny, Polymorphism, Single Nucleotide, Genome, Africa, Asia, Southeastern, Gene Flow, Genetic Variation, General Science & Technology
Abstract

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Published
2013

18. 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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20. Pervasive incomplete lineage sorting illuminates speciation and selection in primates

Author

Rivas-González, Iker, Rousselle, Marjolaine, Li, Fang, Zhou, Long, Dutheil, Julien Y., Munch, Kasper, Shao, Yong, Wu, Dongdong, Schierup, Mikkel H., and Zhang, Guojie

Abstract

Incomplete lineage sorting (ILS) causes the phylogeny of some parts of the genome to differ from the species tree. In this work, we investigate the frequencies and determinants of ILS in 29 major ancestral nodes across the entire primate phylogeny. We find up to 64% of the genome affected by ILS at individual nodes. We exploit ILS to reconstruct speciation times and ancestral population sizes. Estimated speciation times are much more recent than genomic divergence times and are in good agreement with the fossil record. We show extensive variation of ILS along the genome, mainly driven by recombination but also by the distance to genes, highlighting a major impact of selection on variation along the genome. In many nodes, ILS is reduced more on the X chromosome compared with autosomes than expected under neutrality, which suggests higher impacts of natural selection on the X chromosome. Finally, we show an excess of ILS in genes with immune functions and a deficit of ILS in housekeeping genes. The extensive ILS in primates discovered in this study provides insights into the speciation times, ancestral population sizes, and patterns of natural selection that shape primate evolution.

Published
2023

21. 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

23. Single-cell analysis maps distinct cellular responses to rhizobia and identifies the novel infection regulator SYMRKL1 inLotus japonicus

Author

Frank, Manuel, primary, Fechete, Lavinia Ioana, additional, Tedeschi, Francesca, additional, Nadzieja, Marcin, additional, Malekzadeh Nørgaard, Malita Malou, additional, Montiel, Jesus, additional, Andersen, Kasper Røjkjær, additional, Schierup, Mikkel H., additional, Reid, Dugald, additional, and Andersen, Stig Uggerhøj, additional

Published
2022
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26. The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

Author

Bergeron, Lucie A, primary, Besenbacher, Søren, additional, Turner, Tychele, additional, Versoza, Cyril J, additional, Wang, Richard J, additional, Price, Alivia Lee, additional, Armstrong, Ellie, additional, Riera, Meritxell, additional, Carlson, Jedidiah, additional, Chen, Hwei-yen, additional, Hahn, Matthew W, additional, Harris, Kelley, additional, Kleppe, April Snøfrid, additional, López-Nandam, Elora H, additional, Moorjani, Priya, additional, Pfeifer, Susanne P, additional, Tiley, George P, additional, Yoder, Anne D, additional, Zhang, Guojie, additional, and Schierup, Mikkel H, additional

Published
2022
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27. Author response: The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

Author

Bergeron, Lucie A, primary, Besenbacher, Søren, additional, Turner, Tychele, additional, Versoza, Cyril J, additional, Wang, Richard J, additional, Price, Alivia Lee, additional, Armstrong, Ellie, additional, Riera, Meritxell, additional, Carlson, Jedidiah, additional, Chen, Hwei-yen, additional, Hahn, Matthew W, additional, Harris, Kelley, additional, Kleppe, April Snøfrid, additional, López-Nandam, Elora H, additional, Moorjani, Priya, additional, Pfeifer, Susanne P, additional, Tiley, George P, additional, Yoder, Anne D, additional, Zhang, Guojie, additional, and Schierup, Mikkel H, additional

Published
2022
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32. Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates

Author

Bergeron, Lucie A., primary, Besenbacher, Søren, additional, Turner, Tychele N., additional, Versoza, Cyril J., additional, Wang, Richard J., additional, Price, Alivia Lee, additional, Armstrong, Ellie, additional, Riera, Meritxell, additional, Carlson, Jedidiah, additional, Chen, Hwei-yen, additional, Hahn, Matthew W., additional, Harris, Kelley, additional, Snøfrid Lo Natalie M Kleppe, April, additional, López-Nandam, Elora H., additional, Moorjani, Priya, additional, Pfeifer, Susanne P., additional, Tiley, George P., additional, Yoder, Anne D., additional, Zhang, Guojie, additional, and Schierup, Mikkel H., additional

Published
2021
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34. Small RNAs in Seminal Plasma as Novel Biomarkers for Germ Cell Tumors

Author

Mørup, Nina, primary, Stakaitis, Rytis, additional, Golubickaite, Ieva, additional, Riera, Meritxell, additional, Dalgaard, Marlene Danner, additional, Schierup, Mikkel H., additional, Jørgensen, Niels, additional, Daugaard, Gedske, additional, Juul, Anders, additional, and Almstrup, Kristian, additional

Published
2021
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36. 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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38. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

Author

Besenbacher, Søren, Liu, Siyang, Izarzugaza, José M. G., Grove, Jakob, Belling, Kirstine, Bork-Jensen, Jette, Huang, Shujia, Als, Thomas D., Li, Shengting, Yadav, Rachita, Rubio-García, Arcadio, Lescai, Francesco, Demontis, Ditte, Rao, Junhua, Ye, Weijian, Mailund, Thomas, Friborg, Rune M., Pedersen, Christian N. S., Xu, Ruiqi, Sun, Jihua, Liu, Hao, Wang, Ou, Cheng, Xiaofang, Flores, David, Rydza, Emil, Rapacki, Kristoffer, Damm Sørensen, John, Chmura, Piotr, Westergaard, David, Dworzynski, Piotr, Sørensen, Thorkild I. A., Lund, Ole, Hansen, Torben, Xu, Xun, Li, Ning, Bolund, Lars, Pedersen, Oluf, Eiberg, Hans, Krogh, Anders, Børglum, Anders D., Brunak, Søren, Kristiansen, Karsten, Schierup, Mikkel H., Wang, Jun, Gupta, Ramneek, Villesen, Palle, and Rasmussen, Simon

Published
2015
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39. Ancestral population genomics: the coalescent hidden Markov model approach

Author

Dutheil, Julien Y., Ganapathy, Ganesh, Hobolth, Asger, Mailund, Thomas, Uyenoyama, Marcy K., and Schierup, Mikkel H.

Subjects
Evolutionary genetics -- Research, Genetic recombination -- Research, Population genetics -- Research, Origin of species -- Research, Biological sciences
Published
2009

40. Expression of distinct self-incompatibility specificities in Arabidopsis thaliana

Author

Boggs, Nathan A., Dwyer, Kathleen G., Shah, Paurush, McCulloch, Amanda A., Bechsgaard, Jesper, Schierup, Mikkel H., Nasrallah, Mikhail E., and Nasrallah, June B.

Subjects
Arabidopsis thaliana -- Genetic aspects, Gene expression -- Research, Plant breeding -- Research, Plants -- Reproduction, Plants -- Research, Biological sciences
Published
2009

42. Selection at work in self-incompatible Arabidopsis lyrata. II. Spatial distribution of S haplotypes in Iceland

Author

Schierup, Mikkel H., Bechsgaard, Jesper S., and Christiansen, Freddy B.

Subjects
Arabidopsis -- Genetic aspects, Haplotypes -- Identification and classification, Plants -- Self-incompatibility, Plants -- Genetic aspects, Biological sciences
Abstract

We survey the distribution of haplotypes at the self-incompatibility (SI) locus of Arabidopsis lyrata (Brassicaceae) at 12 locations spread over the species' natural distribution in Iceland. Previous investigations of the system have identified 34 functionally different S haplotypes maintained by frequency-dependent selection and arranged them into four classes of dominance in their phenotypic expression. On the basis of this model of dominance and the island model of population subdivision, we compare the distribution of S haplotypes with that expected from population genetic theory. We observe 18 different S haplotypes, recessive haplotypes being more common than dominant ones, and dominant ones being shared by fewer populations. As expected, differentiation, although significant, is very low at the S locus even over distances of up to 300 km. The frequency of the most recessive haplotype is slightly larger than expected for a panmictic population, but consistent with a subdivided population with the observed differentiation. Frequencies in nature reflect effects of segregation distortion previously observed in controlled crosses. The dynamics of the S-locus variation are, however, well represented by a 12-island model and our simplified model of dominance interactions.

Published
2008

43. Selection at work in self-incompatible Arabidopsis lyrata: mating patterns in a natural population

Author

Schierup, Mikkel H., Bechsgaard, Jesper S., Nielsen, Lene H., and Christiansen, Freddy B.

Subjects
Arabidopsis -- Genetic aspects, Arabidopsis -- Research, Courtship of animals -- Research, Haplotypes -- Research, Plants -- Self-incompatibility, Plants -- Research, Biological sciences
Abstract

Identification and characterization of the self-incompatibility genes in Brassicaceae species now allow typing of self-incompatibility haplotypes in natural populations. In this study we sampled and mapped all 88 individuals in a small population of Arabidopsis lyrata from Iceland. The self-incompatibility haplotypes at the SRK gene were typed for all the plants and some of their progeny and used to investigate the realized mating patterns in the population. The observed frequencies of haplotypes were found to change considerably from the parent generation to the offspring generation around their deterministic equilibria as determined from the known dominance relations among haplotypes. We provide direct evidence that the incompatibility system discriminates against matings among adjacent individuals. Multiple paternity is very common, causing mate availability among progeny of a single mother to be much larger than expected for single paternity.

Published
2006

45. Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata

Author

Charlesworth, Deborah, Mable, Barbara K., Schierup, Mikkel H., Bartolome, Carolina, and Awadalla, Philip

Subjects
Proteins -- Genetic aspects, Population genetics -- Research, Arabidopsis -- Genetic aspects, Genetics -- Research, Biological sciences
Abstract

We report studies of seven members of the S-domain gene family in Arabidopsis lyrata, a member of the Brassicaceae that has a sporophytic self-incompatibility (SI) system. Orthologs for five loci are identifiable in the self-compatible relative A. thaliana. Like the Brassica stigmatic incompatibility protein locus (SRK), some of these genes have kinase domains. We show that several of these genes are unlinked to the putative A. lyrata SRK Aly13. These genes have much lower nonsynonymous and synonymous polymorphism than Aly13 in the S-domains within natural populations, and differentiation between populations is higher, consistent with balancing selection at the Aly13 locus. One gene (Aly8) is linked to Aly13 and has high diversity. No departures from neutrality were detected for any of the loci. Comparing different loci within A. lyrata, sites corresponding to hypervariable regions in the Brassica S-loci (SLG and SRK) and in comparable regions of Aly13 have greater replacement site divergence than the rest of the S-domain. This suggests that the high polymorphism in these regions of incompatibility loci is due to balancing selection acting on sites within or near these regions, combined with low selective constraints.

Published
2003

47. The bonobo genome compared with the chimpanzee and human genomes

Author

Prüfer, Kay, Munch, Kasper, Hellmann, Ines, Akagi, Keiko, Miller, Jason R., Walenz, Brian, Koren, Sergey, Sutton, Granger, Kodira, Chinnappa, Winer, Roger, Knight, James R., Mullikin, James C., Meader, Stephen J., Ponting, Chris P., Lunter, Gerton, Higashino, Saneyuki, Hobolth, Asger, Dutheil, Julien, Karakoç, Emre, Alkan, Can, Sajjadian, Saba, Catacchio, Claudia Rita, Ventura, Mario, Marques-Bonet, Tomas, Eichler, Evan E., André, Claudine, Atencia, Rebeca, Mugisha, Lawrence, Junhold, Jörg, Patterson, Nick, Siebauer, Michael, Good, Jeffrey M., Fischer, Anne, Ptak, Susan E., Lachmann, Michael, Symer, David E., Mailund, Thomas, Schierup, Mikkel H., Andrés, Aida M., Kelso, Janet, and Pääbo, Svante

Published
2012
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48. Insights into hominid evolution from the gorilla genome sequence

Author

Scally, Aylwyn, Dutheil, Julien Y., Hillier, LaDeana W., Jordan, Gregory E., Goodhead, Ian, Herrero, Javier, Hobolth, Asger, Lappalainen, Tuuli, Mailund, Thomas, Marques-Bonet, Tomas, McCarthy, Shane, Montgomery, Stephen H., Schwalie, Petra C., Tang, Amy Y., Ward, Michelle C., Xue, Yali, Yngvadottir, Bryndis, Alkan, Can, Andersen, Lars N., Ayub, Qasim, Ball, Edward V., Beal, Kathryn, Bradley, Brenda J., Chen, Yuan, Clee, Chris M., Fitzgerald, Stephen, Graves, Tina A., Gu, Yong, Heath, Paul, Heger, Andreas, Karakoc, Emre, Kolb-Kokocinski, Anja, Laird, Gavin K., Lunter, Gerton, Meader, Stephen, Mort, Matthew, Mullikin, James C., Munch, Kasper, O’Connor, Timothy D., Phillips, Andrew D., Prado-Martinez, Javier, Rogers, Anthony S., Sajjadian, Saba, Schmidt, Dominic, Shaw, Katy, Simpson, Jared T., Stenson, Peter D., Turner, Daniel J., Vigilant, Linda, Vilella, Albert J., Whitener, Weldon, Zhu, Baoli, Cooper, David N., de Jong, Pieter, Dermitzakis, Emmanouil T., Eichler, Evan E., Flicek, Paul, Goldman, Nick, Mundy, Nicholas I., Ning, Zemin, Odom, Duncan T., Ponting, Chris P., Quail, Michael A., Ryder, Oliver A., Searle, Stephen M., Warren, Wesley C., Wilson, Richard K., Schierup, Mikkel H., Rogers, Jane, Tyler-Smith, Chris, and Durbin, Richard

Published
2012
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49. Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes

Author

Schierup, Mikkel H., Mikkelsen, Anders M., and Hein, Jotun

Subjects
Genetic recombination -- Physiological aspects, Major histocompatibility complex -- Genetic aspects, Phylogeny -- Genetic aspects, Biological sciences
Abstract

Using a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.

Published
2001

50. Intrahaplotype polymorphism at the Brassica S locus

Author

Miege, Christine, Ruffio-Chable, Veronique, Schierup, Mikkel H., Cabrillac, Didier, Dumas, Christian, Gaude, Thierry, and Cock, J. Mark

Subjects
Protein kinases -- Research, Brassica -- Research, Haplotypes -- Research, Biological sciences
Abstract

The S locus receptor kinase and the S locus glycoproteins are encoded by genes located at the S locus, which controls the self-incompatibility response in Brassica. In class II self-incompatibility haplotypes, S locus glycoproteins can be encoded by two different genes, SLGA and SLGB. In this study, we analyzed the sequences of these genes in several independently isolated plants, all of which carry the same S haplotype ([S.sub.2]). Two groups of [S.sub.2] haplotypes could be distinguished depending on whether SRK was associated with SLGA or SLGB. Surprisingly, SRK alleles from the two groups could be distinguished at the sequence level, suggesting that recombination rarely occurs between haplotypes of the two groups. An analysis of the distribution of polymorphisms along the S domain of SRK showed that hypervariable domains I and II tend to be conserved within haplotypes but to be highly variable between haplotypes. This is consistent with these domains playing a role in the determination of haplotype specificity.

Published
2001

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