Browsing by Author "Haussler, David"

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    29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.
    (PloS one, 2012-01) Lowe, Craig B; Haussler, David
    Recent research supports the view that changes in gene regulation, as opposed to changes in the genes themselves, play a significant role in morphological evolution. Gene regulation is largely dependent on transcription factor binding sites. Researchers are now able to use the available 29 mammalian genomes to measure selective constraint at the level of binding sites. This detailed map of constraint suggests that mammalian genomes co-opt fragments of mobile elements to act as gene regulatory sequence on a large scale. In the human genome we detect over 280,000 putative regulatory elements, totaling approximately 7 Mb of sequence, that originated as mobile element insertions. These putative regulatory regions are conserved non-exonic elements (CNEEs), which show considerable cross-species constraint and signatures of continued negative selection in humans, yet do not appear in a known mature transcript. These putative regulatory elements were co-opted from SINE, LINE, LTR and DNA transposon insertions. We demonstrate that at least 11%, and an estimated 20%, of gene regulatory sequence in the human genome showing cross-species conservation was co-opted from mobile elements. The location in the genome of CNEEs co-opted from mobile elements closely resembles that of CNEEs in general, except in the centers of the largest gene deserts where recognizable co-option events are relatively rare. We find that regions of certain mobile element insertions are more likely to be held under purifying selection than others. In particular, we show 6 examples where paralogous instances of an often co-opted mobile element region define a sequence motif that closely matches a transcription factor's binding profile.
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    A high-resolution map of human evolutionary constraint using 29 mammals.
    (Nature, 2011-10-12) Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; Kheradpour, Pouya; Ernst, Jason; Jordan, Gregory; Mauceli, Evan; Ward, Lucas D; Lowe, Craig B; Holloway, Alisha K; Clamp, Michele; Gnerre, Sante; Alföldi, Jessica; Beal, Kathryn; Chang, Jean; Clawson, Hiram; Cuff, James; Di Palma, Federica; Fitzgerald, Stephen; Flicek, Paul; Guttman, Mitchell; Hubisz, Melissa J; Jaffe, David B; Jungreis, Irwin; Kent, W James; Kostka, Dennis; Lara, Marcia; Martins, Andre L; Massingham, Tim; Moltke, Ida; Raney, Brian J; Rasmussen, Matthew D; Robinson, Jim; Stark, Alexander; Vilella, Albert J; Wen, Jiayu; Xie, Xiaohui; Zody, Michael C; Broad Institute Sequencing Platform and Whole Genome Assembly Team; Baldwin, Jen; Bloom, Toby; Chin, Chee Whye; Heiman, Dave; Nicol, Robert; Nusbaum, Chad; Young, Sarah; Wilkinson, Jane; Worley, Kim C; Kovar, Christie L; Muzny, Donna M; Gibbs, Richard A; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team; Cree, Andrew; Dihn, Huyen H; Fowler, Gerald; Jhangiani, Shalili; Joshi, Vandita; Lee, Sandra; Lewis, Lora R; Nazareth, Lynne V; Okwuonu, Geoffrey; Santibanez, Jireh; Warren, Wesley C; Mardis, Elaine R; Weinstock, George M; Wilson, Richard K; Genome Institute at Washington University; Delehaunty, Kim; Dooling, David; Fronik, Catrina; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Minx, Patrick; Sodergren, Erica; Birney, Ewan; Margulies, Elliott H; Herrero, Javier; Green, Eric D; Haussler, David; Siepel, Adam; Goldman, Nick; Pollard, Katherine S; Pedersen, Jakob S; Lander, Eric S; Kellis, Manolis
    The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
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    Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
    (Gigascience, 2013-07-22) Bradnam, Keith R; Fass, Joseph N; Alexandrov, Anton; Baranay, Paul; Bechner, Michael; Birol, Inanç; Boisvert, Sébastien; Chapman, Jarrod A; Chapuis, Guillaume; Chikhi, Rayan; Chitsaz, Hamidreza; Chou, Wen-Chi; Corbeil, Jacques; Del Fabbro, Cristian; Docking, T Roderick; Durbin, Richard; Earl, Dent; Emrich, Scott; Fedotov, Pavel; Fonseca, Nuno A; Ganapathy, Ganeshkumar; Gibbs, Richard A; Gnerre, Sante; Godzaridis, Elénie; Goldstein, Steve; Haimel, Matthias; Hall, Giles; Haussler, David; Hiatt, Joseph B; Ho, Isaac Y; Howard, Jason; Hunt, Martin; Jackman, Shaun D; Jaffe, David B; Jarvis, Erich D; Jiang, Huaiyang; Kazakov, Sergey; Kersey, Paul J; Kitzman, Jacob O; Knight, James R; Koren, Sergey; Lam, Tak-Wah; Lavenier, Dominique; Laviolette, François; Li, Yingrui; Li, Zhenyu; Liu, Binghang; Liu, Yue; Luo, Ruibang; Maccallum, Iain; Macmanes, Matthew D; Maillet, Nicolas; Melnikov, Sergey; Naquin, Delphine; Ning, Zemin; Otto, Thomas D; Paten, Benedict; Paulo, Octávio S; Phillippy, Adam M; Pina-Martins, Francisco; Place, Michael; Przybylski, Dariusz; Qin, Xiang; Qu, Carson; Ribeiro, Filipe J; Richards, Stephen; Rokhsar, Daniel S; Ruby, J Graham; Scalabrin, Simone; Schatz, Michael C; Schwartz, David C; Sergushichev, Alexey; Sharpe, Ted; Shaw, Timothy I; Shendure, Jay; Shi, Yujian; Simpson, Jared T; Song, Henry; Tsarev, Fedor; Vezzi, Francesco; Vicedomini, Riccardo; Vieira, Bruno M; Wang, Jun; Wang, Jun; Worley, Kim C; Yin, Shuangye; Yiu, Siu-Ming; Yuan, Jianying; Zhang, Guojie; Zhang, Hao; Zhou, Shiguo; Korf, Ian F
    BACKGROUND: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. RESULTS: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. CONCLUSIONS: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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    Comparative genomics reveals insights into avian genome evolution and adaptation.
    (Science, 2014-12-12) Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Avian Genome Consortium; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun
    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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    Endangered species hold clues to human evolution.
    (The Journal of heredity, 2010-07) Lowe, Craig B; Bejerano, Gill; Salama, Sofie R; Haussler, David
    We report that 18 conserved, and by extension functional, elements in the human genome are the result of retroposon insertions that are evolving under purifying selection in mammals. We show evidence that 1 of the 18 elements regulates the expression of ASXL3 during development by encoding an alternatively spliced exon that causes nonsense-mediated decay of the transcript. The retroposon that gave rise to these functional elements was quickly inactivated in the mammalian ancestor, and all traces of it have been lost due to neutral decay. However, the tuatara has maintained a near-ancestral version of this retroposon in its extant genome, which allows us to connect the 18 human elements to the evolutionary events that created them. We propose that conservation efforts over more than 100 years may not have only prevented the tuatara from going extinct but could have preserved our ability to understand the evolutionary history of functional elements in the human genome. Through simulations, we argue that species with historically low population sizes are more likely to harbor ancient mobile elements for long periods of time and in near-ancestral states, making these species indispensable in understanding the evolutionary origin of functional elements in the human genome.
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    Feather development genes and associated regulatory innovation predate the origin of Dinosauria.
    (Molecular biology and evolution, 2015-01) Lowe, Craig B; Clarke, Julia A; Baker, Allan J; Haussler, David; Edwards, Scott V
    The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.
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    Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53
    (Proceedings of the National Academy of Sciences, 2007-11-20) Wang, Ting; Zeng, Jue; Lowe, Craig B; Sellers, Robert G; Salama, Sofie R; Yang, Min; Burgess, Shawn M; Brachmann, Rainer K; Haussler, David
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    The birds of Genome10K
    (GigaScience, 2014) OBrien, Stephen J; Haussler, David; Ryder, Oliver
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    The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science.
    (Neoplasia (New York, N.Y.), 2023-01) Lilly, Jena V; Rokita, Jo Lynne; Mason, Jennifer L; Patton, Tatiana; Stefankiewiz, Stephanie; Higgins, David; Trooskin, Gerri; Larouci, Carina A; Arya, Kamnaa; Appert, Elizabeth; Heath, Allison P; Zhu, Yuankun; Brown, Miguel A; Zhang, Bo; Farrow, Bailey K; Robins, Shannon; Morgan, Allison M; Nguyen, Thinh Q; Frenkel, Elizabeth; Lehmann, Kaitlin; Drake, Emily; Sullivan, Catherine; Plisiewicz, Alexa; Coleman, Noel; Patterson, Luke; Koptyra, Mateusz; Helili, Zeinab; Van Kuren, Nicholas; Young, Nathan; Kim, Meen Chul; Friedman, Christopher; Lubneuski, Alex; Blackden, Christopher; Williams, Marti; Baubet, Valerie; Tauhid, Lamiya; Galanaugh, Jamie; Boucher, Katie; Ijaz, Heba; Cole, Kristina A; Choudhari, Namrata; Santi, Mariarita; Moulder, Robert W; Waller, Jonathan; Rife, Whitney; Diskin, Sharon J; Mateos, Marion; Parsons, Donald W; Pollack, Ian F; Goldman, Stewart; Leary, Sarah; Caporalini, Chiara; Buccoliero, Anna Maria; Scagnet, Mirko; Haussler, David; Hanson, Derek; Firestein, Ron; Cain, Jason; Phillips, Joanna J; Gupta, Nalin; Mueller, Sabine; Grant, Gerald; Monje-Deisseroth, Michelle; Partap, Sonia; Greenfield, Jeffrey P; Hashizume, Rintaro; Smith, Amy; Zhu, Shida; Johnston, James M; Fangusaro, Jason R; Miller, Matthew; Wood, Matthew D; Gardner, Sharon; Carter, Claire L; Prolo, Laura M; Pisapia, Jared; Pehlivan, Katherine; Franson, Andrea; Niazi, Toba; Rubin, Josh; Abdelbaki, Mohamed; Ziegler, David S; Lindsay, Holly B; Stucklin, Ana Guerreiro; Gerber, Nicolas; Vaske, Olena M; Quinsey, Carolyn; Rood, Brian R; Nazarian, Javad; Raabe, Eric; Jackson, Eric M; Stapleton, Stacie; Lober, Robert M; Kram, David E; Koschmann, Carl; Storm, Phillip B; Lulla, Rishi R; Prados, Michael; Resnick, Adam C; Waanders, Angela J
    Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.
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    The genome of the green anole lizard and a comparative analysis with birds and mammals.
    (Nature, 2011-08-31) Alföldi, Jessica; Di Palma, Federica; Grabherr, Manfred; Williams, Christina; Kong, Lesheng; Mauceli, Evan; Russell, Pamela; Lowe, Craig B; Glor, Richard E; Jaffe, Jacob D; Ray, David A; Boissinot, Stephane; Shedlock, Andrew M; Botka, Christopher; Castoe, Todd A; Colbourne, John K; Fujita, Matthew K; Moreno, Ricardo Godinez; ten Hallers, Boudewijn F; Haussler, David; Heger, Andreas; Heiman, David; Janes, Daniel E; Johnson, Jeremy; de Jong, Pieter J; Koriabine, Maxim Y; Lara, Marcia; Novick, Peter A; Organ, Chris L; Peach, Sally E; Poe, Steven; Pollock, David D; de Queiroz, Kevin; Sanger, Thomas; Searle, Steve; Smith, Jeremy D; Smith, Zachary; Swofford, Ross; Turner-Maier, Jason; Wade, Juli; Young, Sarah; Zadissa, Amonida; Edwards, Scott V; Glenn, Travis C; Schneider, Christopher J; Losos, Jonathan B; Lander, Eric S; Breen, Matthew; Ponting, Chris P; Lindblad-Toh, Kerstin
    The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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    Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.
    (Proceedings of the National Academy of Sciences of the United States of America, 2007-05) Lowe, Craig B; Bejerano, Gill; Haussler, David
    At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a handful of cases where mobile element insertions have resulted in the introduction of novel conserved nonexonic elements. Here, we present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often located in gene deserts and show a strong preference for residing closest to genes involved in development and transcription regulation. In particular, constrained nonexonic elements with clear repetitive origins are located near genes involved in cell adhesion, including all characterized cellular members of the reelin-signaling pathway. Overall, we find that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.
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    Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
    (Science, 2014-12-12) Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A
    To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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    Three periods of regulatory innovation during vertebrate evolution.
    (Science (New York, N.Y.), 2011-08) Lowe, Craig B; Kellis, Manolis; Siepel, Adam; Raney, Brian J; Clamp, Michele; Salama, Sofie R; Kingsley, David M; Lindblad-Toh, Kerstin; Haussler, David
    The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
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    Whole-genome analyses resolve early branches in the tree of life of modern birds.
    (Science, 2014-12-12) Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon YW; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Suh, Alexander; Weber, Claudia C; da Fonseca, Rute R; Li, Jianwen; Zhang, Fang; Li, Hui; Zhou, Long; Narula, Nitish; Liu, Liang; Ganapathy, Ganesh; Boussau, Bastien; Bayzid, Md Shamsuzzoha; Zavidovych, Volodymyr; Subramanian, Sankar; Gabaldón, Toni; Capella-Gutiérrez, Salvador; Huerta-Cepas, Jaime; Rekepalli, Bhanu; Munch, Kasper; Schierup, Mikkel; Lindow, Bent; Warren, Wesley C; Ray, David; Green, Richard E; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Li, Shengbin; Li, Ning; Huang, Yinhua; Derryberry, Elizabeth P; Bertelsen, Mads Frost; Sheldon, Frederick H; Brumfield, Robb T; Mello, Claudio V; Lovell, Peter V; Wirthlin, Morgan; Schneider, Maria Paula Cruz; Prosdocimi, Francisco; Samaniego, José Alfredo; Vargas Velazquez, Amhed Missael; Alfaro-Núñez, Alonzo; Campos, Paula F; Petersen, Bent; Sicheritz-Ponten, Thomas; Pas, An; Bailey, Tom; Scofield, Paul; Bunce, Michael; Lambert, David M; Zhou, Qi; Perelman, Polina; Driskell, Amy C; Shapiro, Beth; Xiong, Zijun; Zeng, Yongli; Liu, Shiping; Li, Zhenyu; Liu, Binghang; Wu, Kui; Xiao, Jin; Yinqi, Xiong; Zheng, Qiuemei; Zhang, Yong; Yang, Huanming; Wang, Jian; Wang, Jian; Smeds, Linnea; Rheindt, Frank E; Braun, Michael; Fjeldsa, Jon; Orlando, Ludovic; Barker, F Keith; Jønsson, Knud Andreas; Johnson, Warren; Koepfli, Klaus-Peter; O'Brien, Stephen; Haussler, David; Ryder, Oliver A; Rahbek, Carsten; Willerslev, Eske; Graves, Gary R; Glenn, Travis C; McCormack, John; Burt, Dave; Ellegren, Hans; Alström, Per; Edwards, Scott V; Stamatakis, Alexandros; Mindell, David P; Cracraft, Joel; Braun, Edward L; Warnow, Tandy; Jun, Wang; Gilbert, M Thomas P; Zhang, Guojie
    To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.