Branching out: what omics can tell us about primate evolution
作者： Lukas FK Kuderna , Paula Esteller-Cucala , Tomas Marques-Bonet
DOI: 10.1016/J.GDE.2020.06.006
关键词: Context (language use) 、 Evolutionary biology 、 Comparative genomics 、 Genome 、 Biology 、 Primate evolution
摘要: The study of primate comparative genomics has long been a focus research, particularly in the context understanding human evolutionary history. Recently, high-throughput methods have become accessible that allow us to tackle these questions at scale by comparing genomes within and between species, or looking gene regulatory expression changes species tissues. This burst large-scale genomic studies drastically increased resolution which we are now able understand forces acting upon our own species. Furthermore, drop sequencing costs made it possible go beyond generating datasets purely on biology, begin incorporating larger non-human primates. Here, give an overview recent advances across whole radiation.
sci-hub.st 参考文章(68)
Chimpanzee Sequencing and Analysis Consortium Waterson Robert H. waterston@ gs. washington. edu Lander Eric S. lander@ broad. mit. edu Wilson Richard K. rwilson@ watson. wustl. edu, None, Initial sequence of the chimpanzee genome and comparison with the human genome Nature. ,vol. 437, pp. 69- 87 ,(2005) , 10.1038/NATURE04072
Wesley C. Warren, Anna J. Jasinska, Raquel García-Pérez, Hannes Svardal, Chad Tomlinson, Mariano Rocchi, Nicoletta Archidiacono, Oronzo Capozzi, Patrick Minx, Michael J. Montague, Kim Kyung, LaDeana W. Hillier, Milinn Kremitzki, Tina Graves, Colby Chiang, Jennifer Hughes, Nam Tran, Yu Huang, Vasily Ramensky, Oi-wa Choi, Yoon J. Jung, Christopher A. Schmitt, Nikoleta Juretic, Jessica Wasserscheid, Trudy R. Turner, Roger W. Wiseman, Jennifer J. Tuscher, Julie A. Karl, Jörn E. Schmitz, Roland Zahn, David H. O'Connor, Eugene Redmond, Alex Nisbett, Béatrice Jacquelin, Michaela C. Müller-Trutwin, Jason M. Brenchley, Michel Dione, Martin Antonio, Gary P. Schroth, Jay R. Kaplan, Matthew J. Jorgensen, Gregg W.C. Thomas, Matthew W. Hahn, Brian J. Raney, Bronwen Aken, Rishi Nag, Juergen Schmitz, Gennady Churakov, Angela Noll, Roscoe Stanyon, David Webb, Francoise Thibaud-Nissen, Magnus Nordborg, Tomas Marques-Bonet, Ken Dewar, George M. Weinstock, Richard K. Wilson, Nelson B. Freimer, The genome of the vervet (Chlorocebus aethiops sabaeus) Genome Research. ,vol. 25, pp. 1921- 1933 ,(2015) , 10.1101/GR.192922.115
Z. Khan, M. J. Ford, D. A. Cusanovich, A. Mitrano, J. K. Pritchard, Y. Gilad, Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. ,vol. 342, pp. 1100- 1104 ,(2013) , 10.1126/SCIENCE.1242379
Irene Hernando-Herraez, Javier Prado-Martinez, Paras Garg, Marcos Fernandez-Callejo, Holger Heyn, Christina Hvilsom, Arcadi Navarro, Manel Esteller, Andrew J. Sharp, Tomas Marques-Bonet, Dynamics of DNA Methylation in Recent Human and Great Ape Evolution PLoS Genetics. ,vol. 9, pp. e1003763- ,(2013) , 10.1371/JOURNAL.PGEN.1003763
Mark S. Springer, Robert W. Meredith, John Gatesy, Christopher A. Emerling, Jong Park, Daniel L. Rabosky, Tanja Stadler, Cynthia Steiner, Oliver A. Ryder, Jan E. Janečka, Colleen A. Fisher, William J. Murphy, Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix PLOS ONE. ,vol. 7, ,(2012) , 10.1371/JOURNAL.PONE.0049521
, The common marmoset genome provides insight into primate biology and evolution Nature Genetics. ,vol. 46, pp. 850- 857 ,(2014) , 10.1038/NG.3042
Jia Zeng, Genevieve Konopka, Brendan G. Hunt, Todd M. Preuss, Dan Geschwind, Soojin V. Yi, Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. American Journal of Human Genetics. ,vol. 91, pp. 455- 465 ,(2012) , 10.1016/J.AJHG.2012.07.024
Athma A. Pai, Jordana T. Bell, John C. Marioni, Jonathan K. Pritchard, Yoav Gilad, A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLOS Genetics. ,vol. 7, ,(2011) , 10.1371/JOURNAL.PGEN.1001316
Kay Prüfer, Kasper Munch, Ines Hellmann, Keiko Akagi, Jason R. Miller, Brian Walenz, Sergey Koren, Granger Sutton, Chinnappa Kodira, Roger Winer, James R. Knight, James C. Mullikin, Stephen J. Meader, Chris P. Ponting, Gerton Lunter, Saneyuki Higashino, Asger Hobolth, Julien Dutheil, Emre Karakoç, Can Alkan, Saba Sajjadian, Claudia Rita Catacchio, Mario Ventura, Tomas Marques-Bonet, Evan E. Eichler, Claudine André, Rebeca Atencia, Lawrence Mugisha, Jörg Junhold, Nick Patterson, Michael Siebauer, Jeffrey M. Good, Anne Fischer, Susan E. Ptak, Michael Lachmann, David E. Symer, Thomas Mailund, Mikkel H. Schierup, Aida M. Andrés, Janet Kelso, Svante Pääbo, The bonobo genome compared with the chimpanzee and human genomes Nature. ,vol. 486, pp. 527- 531 ,(2012) , 10.1038/NATURE11128
Devin P Locke, LaDeana W Hillier, Wesley C Warren, Kim C Worley, Lynne V Nazareth, Donna M Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A Fulton, Robert S Fulton, Joanne O Nelson, Vincent Magrini, Craig Pohl, Tina A Graves, Chris Markovic, Andy Cree, Huyen H Dinh, Jennifer Hume, Christie L Kovar, Gerald R Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M Kidd, Evan E Eichler, Simon White, Stephen Searle, Albert J Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K Konkel, Jerilyn A Walker, Brygg Ullmer, Mark A Batzer, Arian FA Smit, Robert Hubley, Claudio Casola, Daniel R Schrider, Matthew W Hahn, Victor Quesada, Xose S Puente, Gonzalo R Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S Harris, Webb Miller, Carolin Kosiol, Heather A Lawson, Vikas Taliwal, André L Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D Bustamante, Ryan N Gutenkunst, Thomas Mailund, Julien Y Dutheil, Asger Hobolth, Mikkel H Schierup, Oliver A Ryder, Yuko Yoshinaga, Pieter J De Jong, George M Weinstock, Jeffrey Rogers, Elaine R Mardis, Richard A Gibbs, Richard K Wilson, None, Comparative and demographic analysis of orang-utan genomes. Nature. ,vol. 469, pp. 529- 533 ,(2011) , 10.1038/NATURE09687