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1. E68

Author

Smith, T. P., primary, Haygood, R. A., additional, and Arnold, T., additional

Published
2012
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6. FIELD PERFORMANCE OF DOW AGROSCIENCES' WIDESTRIKETM INSECT PROTECTION AGAINST KEY LEPIDOPTERAN PESTS IN THE MID-SOUTH AND SOUTHEASTERN U.S.

Author

Siebert, M. Willrich, Braxton, L. B., Huckaba, R. M., Walton, L. C., Haygood, R. A., Lassiter, R. B., Haile, F .J., and Thompson, G. D.

Abstract

Field trials conducted during 2006 have indicated WideStrike cotton to be effective against economically important heliothis and secondary lepidopteran pests of cotton in the mid-south and southeastern U.S. WideStrike varieties, including PHY370WR, PHY470WR, PHY480WR, and PHY485WRF were effective against bollworm, Helicoverpa zea, fall armyworm, Spodoptera frugiperda; and soybean looper, Pseudoplusia includens. WideStrike Insect Protection, which delivers two insect control genes, is an excellent tool for cotton producers for management of lepidopteran pests. [ABSTRACT FROM AUTHOR]

Published
2007

8. PERFORMANCE OF WIDESTRIKE™ INSECT PROTECTION FOR CONTROL OF LEPIDOPTERAN PESTS IN ALABAMA FROM 2001 THROUGH 2004.

Author

Smith, R. H., Moore, D. P., Haygood, R. A., Braxton, L. B., and Parker, A. R.

Abstract

WideStrike Insect Protection, developed by Dow AgroSciences LLC, expresses the insecticidal crystal proteins Cry1F and Cry1Ac from the bacterium Bacillus thuringiensis (Bt). Cotton genotype GC510 was transformed to contain the genes that express full-length synthetic protoxins (synpro) of Cry1F or Cry1Ac. Transgenic lines were backcrossed with a non-transgenic elite variety, PSC 355. Subsequently, Cry1F(synpro) and Cry1Ac(synpro) lines were crossed to produce the stacked product MXB-13, or WideStrike Insect Protection. Small plot and larger strip plot trails were conducted in Alabama from 2001 thru 2004 to characterize the efficacy and agronomic performance of the 2 Bt proteins independently as well as when they are expressed together in the varieties PHY 440W and PHY 470 WR. PHY 440 W only expresses the WideStrike Insect Protection trait while PHY 470 WR is a stacked-trait variety which contains the WideStrike Insect Protection trait and RR trait. The trials demonstrated that cotton varieties expressing the WideStrike trait are effective tools in managing southern armyworm (Spodoptera eridania), tobacco budworm (Heliothis virescens[F.]) and bollworm (Helicoverpa zea [Boddie]). Supplemental insecticide applications may be needed to optimize yields when bollworm populations are high. [ABSTRACT FROM AUTHOR]

Published
2005

9. FIELD AND LABORATORY PERFORMANCE OF WIDESTRIKE™ INSECT PROTECTION AGAINST SECONDARY LEPIDOPTERAN PESTS.

Author

Willrich, M. M., Braxton, L. B., Richburg, J. S., Lassiter, R. B., Langston, V. B., Haygood, R. A., Richardson, J. M., Haile, F. J., Huckaba, R. M., Pellow, J. W., Thompson, G. D., and Mueller, J. P.

Abstract

Field and laboratory studies conducted during 2004 have indicated WideStrike cotton to be effective against important secondary lepidopteran pests of cotton. WideStrike varieties, including PHY440W and PHY470WR, were highly effective against fall armyworm, Spodoptera frugiperda; soybean looper, Pseudoplusia includens; cabbage looper, Trichoplusia ni; European corn borer, Ostrinia nubilalis; citrus peelminer, Marmara gulosa; cotton leaf perforator, Bucculatrix thurberiella; and omnivorous leafroller, Playnota stultana. Efficacy of WideStrike was demonstrated against low-level field infestations of black cutworm, Agrotis ipsilon. Results from artificially infested efficacy trials against beet armyworm, Spodoptera exigua, suggest larval survival and foliage feeding may be greater than other species evaluated. The deregulation and registration of WideStrike will enable additional testing under more realistic field conditions. [ABSTRACT FROM AUTHOR]

Published
2005

10. WIDESTIKE™ INSECT PROTECTION AGAINST HELIOTHINE INSECTS.

Author

Huckaba, R. M., Braxton, L. B., Willrich, M. M., Richburg, J. S., Lassiter, R. B., Langston, V. B., Haygood, R. A., Richardson, J. M., Haile, F. J., Pellow, J. W., Thompson, G. D., and Mueller, J. P.

Abstract

Field studies were conducted at seventeen test sites across the cotton belt in 2004. Results showed that cotton expressing the WideStrike™ trait (PHY 440 W and PHY 470 WR) provided very good control of both cotton bollworm (Helicoverpa zea) and tobacco budworm (Heliothis virescens). Management of high populations of cotton bollworm, particularly those sustained over an extended period of time, may require application of a foliar insecticide to prevent exceeding the treatment threshold and to achieve optimum yields in WideStrike cotton. No high populations of tobacco budworm occurred at any of the test sites in 2004, but previous studies indicate no additional insect control measures would be needed to manage this pest in WideStrike cotton. [ABSTRACT FROM AUTHOR]

Published
2005

11. PERFORMANCE OF PHYTOGEN™ COTTON VARIETIES EXPRESSING THE WIDESTRIKE™ INSECT PROTECTION TRAIT WHEN GROWN IN COMMERCIAL TYPE STRIP TRIALS.

Author

Haygood, R. A., Parker, A. R., Richburg, J. S., Lassiter, R. B., Braxton, L. B., Huckaba, R. M., Willrich, M. M., Langston, V. B., Haile, F. J ., Richardson, J. M., Thompson, G. D., Mueller, J. P., McPherson, M. G., and Pellow, J. W.

Abstract

WideStrike Insect Protection, developed by Dow AgroSciences LLC, expresses the insecticidal crystal proteins Cry1F and Cry1Ac from the bacterium Bacillus thuringiensis (Bt). Cotton genotype GC510 (Acala) was used in the transformations which allowed for additional selections for improved fiber characteristics. Larger strip plot trials were conducted from North Carolina to Louisiana in 2003 and 2004 to further characterize the efficacy and agronomic performance of the new WideStrike varieties PHY 440 W and PHY 470 WR. The trials demonstrated that varieties expressing the WideStrike trait provide high levels of control of tobacco budworm (Heliothis virescens[F.]), soybean looper (Pseudoplusia includens), cabbage looper (Trichoplusia ni), and fall armyworm (Spodoptera frugiperda) as well as good to excellent control of bollworm (Helicoverpa zea [Boddie]). The PhytoGen cottonseed varieties PHY 440 W and PHY 470 WR showed high yield potential and very good fiber quality in larger blocks in multiple environments. [ABSTRACT FROM AUTHOR]

Published
2005

15. Plant Population and Planting Date Effects on Cotton (Gossypium hirsutum L.) Growth and Yield.

Author

O'Berry, N. B., Faircloth, J. C., Edmisten, K. L., Collins, G. D., Stewart, A. M., Abaye, A. O., Herbert Jr., D. A., and Haygood, R. A.

Subjects
PLANT populations, PLANT population regeneration, EXPERIMENTAL agriculture, COTTON, PLANTING, PLANT fibers, COTTON farmers
Abstract

To reduce seed costs, cotton (Gossypium hirsutum L.) producers aim to reduce plant populations without sacrificing yields. Field experiments examining the impact of plant population and planting date on cotton growth, fruiting, lint yield, and fiber quality were conducted in Virginia and North Carolina in 2005 and 2006, and in Louisiana during 2005. Plant populations of 4.9, 9.8, and 16.4 plants m-2 and two planting dates ranging from 24 April to 5 May and 15 to 25 May were targeted. Actual plant populations achieved were 5.2, 9.2, and 11.2 plants m-2 (Virginia 2005); 5.2, 9.2, and 15.4 plants m-2 (North Carolina 2005); 5.6, 9.5, and 17.1 plants m-2 (Louisiana 2005); 4.9, 6.6, and 12.8 plants m-2 (Virginia 2006); 5.9, 8.9, and 12.8 plants m-2 (North Carolina 2006). In Virginia in 2005 and 2006, the 5.3 plants m-2 population had more apical main-stem nodes than 8.9 and 12.8 plants m-2, and in 2005 had more monopodial and outer position bolls regardless of planting date. Lint yields were highest with populations of 8.9 and 12.8 plants m-2 in Virginia and North Carolina compared to 5.3 plants m-2, while in Louisiana the highest yields resulted from 5.8 and 9.5 plants m-2 compared to 17.1 plants m-2. In Virginia and North Carolina a maximum of 118 heat units accumulated between planting dates, while 270 heat units accumulated in Louisiana. Regardless of plant population, cotton planted early (1 May) in Louisiana yielded higher than the late planted (21 May). However, there were no yield differences due to planting date in Virginia and North Carolina. In regions where few heats units accumulate early in the season, earlier planting appears to be of little benefit, while earlier planting may increase yields when a significantly larger amount of heat units accumulate near planting. [ABSTRACT FROM AUTHOR]

Published
2008

18. PERFORMANCE OF PHYTOGEN® VARIETIES PHY 370 WR AND PHY 485 WRF IN VARIOUS ENVIRONMENTS.

Author

Haygood, R. A., Parker, A. R., Miller, Herbert T., Jost, Philip H., Reginelli, Le L., McPherson, Mustafa, and Pellow, John W.

Abstract

An abstract of the article "Performance of Phytogen® Varieties PHY 370 WR and PHY 485 WRF in Various Environments," by R. A. Haygood, Philip H. Jost and Herbert T. Miller is presented.

Published
2008

19. PERFORMANCE OF PHYTOGEN® COTTON VARIETIES IN ON FARM INNOVATION TRIALS FROM THE NORTH AND SOUTH DELTA IN 2007.

Author

Parker, A. R., Reginelli, Le L., and Haygood, R. A.

Abstract

The article presents a study which demonstrated the high yield performance and good fiber quality of Phytogen varieties on the on-farm trial being conducted in 2007. It relates that the various substances provided high levels of control of insects such as the tobacco budworm, cabbage looper, southern armyworm, bollworm and soybean looper. In addition, it affirms that the Phytogen varieties have shown good potentialities as compared to other leading market varities. Futhermore, it provides several charts which shows a record of data results during the experiment.

Published
2008

20. EFFECT OF MEPIQUAT CHLORIDE AND PLANTING RATES ON THE GROWTH, YIELDS AND LINT QUALITY OF THE NEW PHYTOGEN™ PHY 400 SERIES.

Author

Haygood, R. A., Barber, Thomas, Steve M. Brown, Craig, C. Chism, Jones, Michael A., Lemon, Robert G., Monks, C. Dale, and Phipps, Bobby J.

Abstract

University trials, large strip trials and commercial plantings have clearly demonstrated the high yield potential of the PhytoGen PHY 400 series which includes PHY 440 W, PHY 470 WR, PHY480 WR, PHY 475 WRF and PHY 485 WRF. To address management questions often asked about new varieties by cotton advisors and growers, 7 trials were initiated with Extension Cotton Specialists to determine the effect of 1X and ½X seeding rates as well as four mepiquat chloride (MC) application scenarios on the yield, growth and lint quality of this series (Tables 1 and 2). All experiments were conducted using the same factorial protocol with either PHY 475 WRF (6 trials) or PHY 485 WRF (MO trial). The "as needed" MC applications were applied as determined by the investigator based on plant development throughout the season. In most trials, data was collected to document first fruiting branch, node above white flower (NAWF) (as the crop neared physiological cutout), plant height (at mid to late season), total nodes, lint yield and quality (based on HVI analysis). Locations of the trials as well as the data collected are provided in Table 3. [ABSTRACT FROM AUTHOR]

Published
2007

21. PERFORMANCE OF PHY 410 R AND PHY 470 WR EXPRESSING THE WIDESTRIKE™ INSECT PROTECTION TRAIT IN 2005 STRIP TRIALS.

Author

Haygood, R. A., Braxton, L. B., Huckaba, R. M., Lassiter, R. B., Parker, A. R., Richardson, J. M., Richburg, J. S., Thompson, G. D., Walton, L. C., Haile, F. J., and Siebert, M. W.

Abstract

An abstract of the study "Performance of PHY 410 R and PHY 470 WR Expressing the Widestrike Insect Protection Trait in 2005 Strip Trials," by R. A. Haygood, L. B. Braxton, and R. M. Huckaba is presented.

Published
2006

22. Standardization of Performance Tests: A Proposal for Further Steps.

Author

TECHNISCHE HOCHSCHULE AACHEN (GERMANY F R) INST FOR PSYCHOLOGY, Sanders,A F, Haygood,R C, Schroiff,H W, Wauschkuhn,C H, TECHNISCHE HOCHSCHULE AACHEN (GERMANY F R) INST FOR PSYCHOLOGY, Sanders,A F, Haygood,R C, Schroiff,H W, and Wauschkuhn,C H

Abstract

This report summarizes the results of Phase I of a study on the feasibility and development of a standardized task battery for measurement of human performance. A major problem today in human performance research is that researches have used a variety of experimental methods and tasks. Even when the task is ostensibly the same (e.g., multiple-choice reaction time), experimenters have used different task parameters, equipment, stimuli, instructions, and so forth. This lack of standardization has created several problems for those who wish to use the results for practical decision making. For example there are no norms for the various experimental tasks. Furthermore, when there are differences in outcomes, they are often attributed to differences in method, without definitive evidence of the relevant differences are. In fact, the documentation regarding procedures, equipment, subjects, and independent variables has frequently been inadequate to the degree that exact replication of many experiments is impossible. Finally, there is a widespread complaint that the methods and tasks used in the laboratory are so simple and artificial that they have little or no applicability to real world tasks. Certainly there has been little attempt to relate laboratory tasks to real-life tasks or even to each other.

Published
1986

29. UTILIZATION OF PRECISION AGRICULTURE TO DEVELOP SITE SPECIFIC TREATMENT OF NEMATODES IN THE NORTH DELTA.

Author

Haygood, R. A., Fordice, A. J., Busacca, J. J., Kirkpatrick, Terry L., and Monfort, W. Scott

Abstract

Nematodes are not evenly distributed in a field. Recent research in LA, AR and GA indicated that root-knot nematodes cause more damage and subsequent greater yield reductions in low-density sandy soils with lower electrical conductivity (Ec) than in heavier clay soils with higher Ec values. This information is being used to develop methods to apply Telone® II in those areas of the field which should result in the greatest return on investment. Technologies used to map Ec ranges have been developed to determine and map "responsive" soils in the field. GPS guided, precision application equipment can then be used to apply Telone only to those areas of the field where a positive response is most likely to occur. This was the case in several trials conducted in AR. However, this technology is not applicable for all root knot nematode infested fields which was the case in a MO trial due to high nematode pressure across the field with a high sand content soil. ®Trademark of Dow AgroSciences LLC. Telone is a Restricted Use Pesticide. In Florida, refer to the 24(c) Telone specimen label for restrictions in certain counties. Telone is not registered for sale or use in all states. Contact your state pesticide regulatory agency to determine if a product is registered for sale or use in your state. Always read and follow label directions. [ABSTRACT FROM AUTHOR]

Published
2010

30. PERFORMANCE OF DOW AGROSCIENCES' SULFOXAFLOR INSECTICIDE AGAINST TARNISHED PLANT BUG, LYGUS LINEOLARIS, IN MID-SOUTH COTTON.

Author

Siebert, M. Willrich, Walton, L. C, Lassiter, R. B., Haygood, R. A., Thomas, J. D., and Richburg, J. S.

Abstract

Sulfoxaflor is a new proprietary insecticide within a novel chemical class developed by Dow AgroSciences. Sulfoxaflor insecticide is active against a broad range of sap-feeding insects including aphids, Aphis gosypii, Tarnished plant bugs, Lygus lineolaris, whiteflies, planthoppers, and scales. Research has demonstrated sulfoxaflor to be active against target pests at low rates, to provide fast knockdown, and extended residual control. Sulfoxaflor was characterized for activity against tarnished plant bug, Lygus lineolaris, in the mid-south U.S. cotton during 2008-2009. A robust testing program included 32 trials in 10 locations, conducted by both public and private researchers. Sulfoxaflor insecticide was evaluated over a wide range of environmental conditions and tarnished plant bug infestation levels. Results from two years of testing demonstrated sulfoxaflor insecticide (0.045 lb ai/acre) provided knockdown of tarnished plant bug infestations at ≤ 5 d and residual control for ≥ 7 d. In addition, cotton treated with sulfoxaflor protected lint yield equal to or superior than cotton treated with acephate (1.0 lb ai/acre) in 16 trials. As with most insecticides, the performance of sulfoxaflor in cotton will be dependent upon tarnished plant bug population level and intensity of infestation. Based upon the two years of research, multiple applications of sulfoxaflor may be required and the interval between applications may vary in cotton for tarnished plant bug management. Sulfoxaflor insecticide will have an excellent fit in cotton IPM programs based on the molecule's spectrum and properties, as a rotational partner with other chemistries, and as a tool for management of insect resistant populations. Recommended scouting techniques for tarnished plant bugs and IPM practices should continue to be utilized. Registration of sulfoxaflor for U.S cotton is anticipated in 2012. [ABSTRACT FROM AUTHOR]

Published
2010

31. EFFECT OF PLANTING DATE, VARIETY, AND DEFOLIATION PROGRAM ON YIELD AND FIBER QUALITY.

Author

Dodds, D. M., Koger, C. H., Haygood, R. A., Faircloth, J. C., Jones, M. A., Main, C. L., and Monks, C. D.

Abstract

The objective of this study was to determine the effect of different levels of leaf hairiness, planting date, defoliation timing and program on cotton lint yield and fiber quality. Varieties selected for the study were PHY 485 WRF (hairy leaf), PHY 375 WRF (semi-smooth leaf) and ST 4357 B2RF (smooth leaf). April and May planting dates were included in the study sites in MS, TN and VA and a May planting date was used in the AL and SC sites. Treatments included 2 defoliation timings of 50 to 60% open bolls and 90 to 100% open bolls and 2 defoliation programs intended to provide marginal or moderate defoliation. The optimum defoliation program consisted of Dropp at 0.1 lb ai/acre + Def 6 EC at 0.75 lb ai/acre + Prep at 1.13 lb ai/acre whereas the moderate defoliation program consisted of Dropp at 0.1 lb ai/acre + Prep at 1.13 lb ai/acre. Standard small plot trial methods were followed using locally recommended agronomic practices. Seed cotton samples were ginned and fiber samples analyzed using HVI to determine gin turnout, micronaire, strength, length, uniformity and leaf content. A randomized complete block experimental design with a factorial arrangement of treatments was utilized for this study. Location was considered a random effect. Data were analyzed as an unbalanced dataset (Spilke et al. 2005) due to three locations having two planting dates and two locations having one planting date and means were separated using Fisher's Protected LSD @ 0.05. In these studies, defoliation was influenced by planting date and defoliation program, but not by leaf hair characteristics. Better defoliation was achieved in the April planted cotton as well as with the optimum defoliation program than that achieved with the later planting interval or sub-optimal defoliation program. Lint yield was affected by variety and defoliation timing. PHY 375 WRF produced significantly higher yields than PHY 485 WRF or ST 4357 B2RF and defoliating at 90% versus 50% open bolls resulted in significantly higher yields. A significant planting date by defoliation program interaction was present. The optimum defoliation program resulted in higher yields in the April planting, but not the May planting. Gin turnout, length, and uniformity were influenced by planting date and variety while defoliation timing and program had no effect. April planted cotton tended to have increased gin turnout, length, and uniformity compared to May planted cotton. PHY 375 WRF, ST 4357 B2RF, and PHY 485 WRF had the highest gin turnout, fiber length, and uniformity, respectively. Micronaire was impacted by planting date, variety and defoliation timing. Strength was only impacted by variety with PHY 485 WRF having the highest strength and ST 4357 B2RF the lowest. April planting resulted in less leaf content in ST 4357 B2RF than the other 2 varieties, but there were no differences among varieties in the May planting. The difference in leaf content in the April planting may have been associated with the smooth leaf of ST 4357 B2RF. Planting in April and defoliating at 90% open bolls resulted in decreased leaf content as compared to planting in April and defoliating at 50% open bolls. Defoliation timing did not affect leaf content in the May planting. In addition, use of the optimum defoliation program caused a significant increase of leaf content in the May planting, but not the April planting dates. These trials will be repeated in order to further determine the effect of variety selection, planting data, defoliation program, and defoliation timing on lint yield and fiber quality. [ABSTRACT FROM AUTHOR]

Published
2009

32. PHY 375 WRF AND PHY 315 RF, TWO NEW EARLY MATURING COTTON VARIETIES FROM PHYTOGEN.

Author

Miller, Herbert T., Jost, Philip H., Parker, A. R., Haygood, R. A., Pellow, John, and McPherson, M.

Abstract

An abstract of the article "PHY 375 WRF and PHY 315 RF, Two New Early Maturing Cotton Varieties From Phytogen," by Herbert T. Miller, Philip H. Jost, A. R. Parker, R. A. Haygood, John Pellow and M. McPherson is presented.

Published
2008

35. WIDESTRIKE*: A NEW STACKED INSECT RESISTANT TRAIT FOR COTTON.

Author

Thompson, G. D., Pellow, J. W., Braxton, L. B., Haygood, R. A., Huckaba, R. M., Lassiter, R. B., Haile, F. J., Wilrich, M. M., Richburg, J. S., and Richardson, J. M.

Abstract

An abstract of the article "Widestrike*: A New Stacked Insect Resistant Trait for Cotton," by G. D. Thompson, J.W. Pellow and R. A. Haygood is presented.

Published
2005

36. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author

Amro Hamdoun, Virginia Brockton, Huyen Dinh, Qiang Tu, Richard O. Hynes, Maria Ina Arnone, Wratko Hlavina, L. Courtney Smith, Mariano A. Loza, David R. Burgess, Matthew P. Hoffman, Florian Raible, Qiu Autumn Yuan, Geoffrey Okwuonu, Mark Y. Tong, Jennifer Hume, Donna Maglott, Manisha Goel, Olivier Fedrigo, Manuel L. Gonzalez-Garay, Celina E. Juliano, Judith Hernandez, Gary M. Wessel, William F. Marzluff, Audrey J. Majeske, Christian Gache, Louise Duloquin, Xingzhi Song, François Lapraz, Fowler J, Alexandre Souvorov, Jared V. Goldstone, Georgia Panopoulou, Sandra Hines, Kyle M. Judkins, Clay Davis, Christine G. Elsik, Paul Kitts, Mariano Loza-Coll, Greg Wray, Taku Hibino, Eric Röttinger, Allison M. Churcher, Annamaria Locascio, Arcady Mushegian, Masashi Kinukawa, Anna Reade, Katherine M. Buckley, I. R. Gibbons, Bert Gold, Aleksandar Milosavljevic, David Epel, Victor D. Vacquier, Ling Ling Pu, Vincenzo Cavalieri, Erin L. Allgood, Lan Zhang, Lynne V. Nazareth, Constantin N. Flytzanis, Ian Bosdet, Yi-Hsien Su, Zeev Pancer, Matthew L. Rowe, Robert C. Angerer, David R. McClay, William H. Klein, Rachel F. Gray, Julian L. Wong, Shunsuke Yaguchi, Robert Bellé, Aaron J. Mackey, Herath Jayantha Gunaratne, Karl Frederik Bergeron, Bruce P. Brandhorst, Greg Murray, Avis H. Cohen, Stephanie Bell, Kristin Tessmar-Raible, Ian K. Townley, Bertrand Cosson, Thomas D. Glenn, Jongmin Nam, Cynthia A. Bradham, Michael Dean, Joseph Chacko, Anthony J. Robertson, Margherita Branno, Valeria Matranga, K. James Durbin, Esther Miranda, Lili Chen, Eran Elhaik, Robert D. Burke, Rita A. Wright, Paola Oliveri, Sandra L. Lee, Gary W. Moy, Alexander E Primus, Shawn S. McCafferty, Cristina Calestani, David A. Garfield, Erica Sodergren, Karen Wilson, Joel Smith, Marco A. Marra, Cynthia Messier, Julia Morales, Kim D. Pruitt, Rachel Thorn, Rachel Gill, John S. Taylor, Mark E. Hahn, Victor Sapojnikov, Meredith Howard-Ashby, Lynne M. Angerer, Maurice R. Elphick, Kathy R. Foltz, Anne Marie Genevière, Justin T. Reese, Blanca E. Galindo, Kim C. Worley, Andrew Leone, Glen Humphrey, Kevin Berney, Olga Ermolaeva, George Miner, David P. Terwilliger, Elly Suk Hen Chow, Lora Lewis, Dan Graur, C. Titus Brown, Gerard Manning, Kevin J. Peterson, Angela Jolivet, Michele K. Anderson, Francesca Rizzo, Ekaterina Voronina, Thierry Lepage, Giorgio Matassi, Antonio Fernandez-Guerra, Mamoru Nomura, Charles A. Whittaker, James R.R. Whittle, James A. Coffman, George M. Weinstock, Mohammed M. Idris, Ashlan M. Musante, Sebastian D. Fugmann, Katherine D. Walton, Sorin Istrail, Shu-Yu Wu, Cerrissa Hamilton, Jonah Cool, Jacqueline E. Schein, Stacey M. Curry, Athula Wikramanayke, Seth Carbonneau, Blair J. Rossetti, Christopher E. Killian, Melissa J. Landrum, Amanda P. Rawson, Jenifer C. Croce, Ryan C. Range, Rahul Satija, John J. Stegeman, Yufeng Shen, Cavit Agca, Terry Gaasterland, Rocky Cheung, Takae Kiyama, Nikki Adams, Jonathan P. Rast, Robert Piotr Olinski, Andrew Cree, Mark Scally, Shuguang Liang, David A. Parker, Rebecca Thomason, Gretchen E. Hofmann, Michelle M. Roux, Ronghui Xu, Robert A. Obar, Enrique Arboleda, Odile Mulner-Lorillon, Shannon Dugan-Rocha, David J. Bottjer, Gabriele Amore, Manoj P. Samanta, Waraporn Tongprasit, Véronique Duboc, La Ronda Jackson, Fred H. Wilt, Viktor Stolc, Anna T. Neill, Michael Raisch, Pei Yun Lee, Jia L. Song, Margaret Morgan, Brian T. Livingston, Sofia Hussain, Zheng Wei, Bryan J. Cole, Tonya F. Severson, Victor V. Solovyev, Finn Hallböök, Donna M. Muzny, Christine A. Byrum, Albert J. Poustka, Xiuqian Mu, Andrew R. Jackson, Shin Heesun, Euan R. Brown, Nansheng Chen, Patrick Cormier, Ralph Haygood, Pedro Martinez, R. Andrew Cameron, D. Wang, Wendy S. Beane, Eric H. Davidson, Christie Kovar, Hemant Kelkar, Charles A. Ettensohn, Sham V. Nair, Robert L. Morris, Stefan C. Materna, Michael C. Thorndyke, Richard A. Gibbs, Dan O Mellott, Department of Physiology and Biophysics, Stony Brook University [The State University of New York] ( SBU ), Astronomy Unit ( AU ), Queen Mary University of London ( QMUL ), Urban and Industrial Air Quality Group, CSIRO Energy Technology, Commonwealth Scientific and Industrial Research Organisation Energy Technology ( CSIRO Energy Technology ), Commonwealth Scientific and Industrial Research Organisation, Center for Polymer Studies ( CPS ), Boston University [Boston] ( BU ), Physics Department [Boston] ( BU-Physics ), Max Planck Institute for Psycholinguistics, Max-Planck-Institut, Department of Biology [Norton], Wheaton College [Norton], Mathematical Institute [Oxford] ( MI ), University of Oxford [Oxford], Centre for the Analysis of Time Series ( CATS ), London School of Economics and Political Science ( LSE ), Thomas Jefferson National Accelerator Facility ( Jefferson Lab ), Thomas Jefferson National Accelerator Facility, Laboratoire d'Energétique et de Mécanique Théorique Appliquée ( LEMTA ), Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Evolution, Génomes et Spéciation ( LEGS ), Centre National de la Recherche Scientifique ( CNRS ), Department of Geology, University of Illinois at Urbana-Champaign [Urbana], Department of Electrical and Computer Engineering [Portland] ( ECE ), Portland State University [Portland] ( PSU ), Saint-Gobain Crystals [USA], SAINT-GOBAIN, Institute for Animal Health ( IAH ), Biotechnology and Biological Sciences Research Council, Center for Agricultural Resources Research, Chinese Academy of Sciences [Changchun Branch] ( CAS ), Ipsen Inc. [Milford] ( Ipsen ), IPSEN, Department of Physics [Berkeley], University of California [Berkeley], Institute for Climate and Atmospheric Science [Leeds] ( ICAS ), University of Leeds, Chung-Ang University ( CAU ), Chung-Ang University [Seoul], Antarctic Climate and Ecosystems Cooperative Research Center ( ACE-CRC ), Institute of Aerodynamics and Fluid Mechanics ( AER ), Technische Universität München [München] ( TUM ), Mer et santé ( MS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Imperial College London, Radio and Atmospheric Sciences Division, National Physical Laboratory [Teddington] ( NPL ), International Research Institute for Climate and Society ( IRI ), Earth Institute at Columbia University, Columbia University [New York]-Columbia University [New York], Soils Group, The Macaulay Institute, Department of Haematology, University of Cambridge [UK] ( CAM ), School of Biology and Biochemistry, Queen's University, Leslie Hill Institute for Plant Conservation ( PCU ), University of Cape Town, Institute for Microelectronics and Microsystems/ Istituto per la Microelettronica e Microsistemi ( IMM ), Consiglio Nazionale delle Ricerche ( CNR ), Laboratoire d'acoustique de l'université du Mans ( LAUM ), Le Mans Université ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Interactive Systems Labs ( ISL ), Carnegie Mellon University [Pittsburgh] ( CMU ), Dalian Institute of Chemical Physics ( DICP ), Architectures, Languages and Compilers to Harness the End of Moore Years ( ALCHEMY ), Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique ( Inria ), Clean Air Task Force ( CATF ), Clean Air Task Force, Space Physics Laboratory, Indian Space Research Organisation ( ISRO ), Centre d'études et de recherches appliquées à la gestion ( CERAG ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Microbiology and Immunology, College of Medicine and Health Sciences-Sultan Qaboos University, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), Department of Biostatistics, University of Michigan [Ann Arbor], Department of Radiation Oncology [Michigan] ( Radonc ), Department of Physics and Astronomy [Leicester], University of Leicester, Informatique, Biologie Intégrative et Systèmes Complexes ( IBISC ), Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut für Meteorologie und Klimaforschung ( IMK ), Karlsruher Institut für Technologie ( KIT ), Physics Department [UNB], University of New Brunswick ( UNB ), Laboratoire Parole et Langage ( LPL ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ), Institut des Sciences Chimiques de Rennes ( ISCR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Ecole Nationale Supérieure de Chimie de Rennes-Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Bioprojet, Laboratoire de Matériaux à Porosité Contrôlée ( LMPC ), Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique ( CNRS ), School of Information Engineering [USTB] ( SIE ), University of Science and Technology Beijing [Beijing] ( USTB ), Laboratory for Atmospheric and Space Physics [Boulder] ( LASP ), University of Colorado Boulder [Boulder], Department of Applied Mathematics [Sheffield], University of Sheffield [Sheffield], School of Mathematics and Statistics [Sheffield] ( SoMaS ), Laboratoire de Mécanique de Lille - FRE 3723 ( LML ), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Centre National de la Recherche Scientifique ( CNRS ), Computer Science Department [UCLA] ( CSD ), University of California at Los Angeles [Los Angeles] ( UCLA ), Développement et évolution ( DE ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie du Développement de Villefranche sur mer ( LBDV ), Laboratoire Pierre Aigrain ( LPA ), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris ( FRDPENS ), Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Mathematics and Statistics [Mac Gill], McGill University, Departamento de Botánica [Comahue], Universidad nacional del Comahue, Bioénergétique Cellulaire et Pathologique ( BECP ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Environnements et Paléoenvironnements OCéaniques ( EPOC ), Observatoire aquitain des sciences de l'univers ( OASU ), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratori Nazionali del Sud ( LNS ), National Institute for Nuclear Physics ( INFN ), Departament de Matemàtiques [Barcelona], Universitat Autònoma de Barcelona [Barcelona] ( UAB ), Max-Planck-Institut für Kohlenforschung (coal research), Institute of Oceanology [CAS] ( IOCAS ), National Chiao Tung University ( NCTU ), Department of Hydrology and Water Resources ( HWR ), University of Arizona, Centre for Educational Technology, Environment Department [York], University of York [York, UK], State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Peking University [Beijing], Department of Physics and Astronomy [Iowa City], University of Iowa [Iowa], NASA Ames Research Center ( ARC ), Department of Materials, Digital Language & Knowledge Contents Research Association ( DICORA ), Hankuk University of Foreign Studies, Department of Physics [Coventry], University of Warwick [Coventry], Space Science and Technology Department [Didcot] ( RAL Space ), STFC Rutherford Appleton Laboratory ( RAL ), Science and Technology Facilities Council ( STFC ) -Science and Technology Facilities Council ( STFC ), Institut de biologie et chimie des protéines [Lyon] ( IBCP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), H M Nautical Almanac Office [RAL] ( HMNAO ), Rutherford Appleton Laboratory, United Kingdom Met Office [Exeter], University College of London [London] ( UCL ), Department of Pathology and Laboratory Medicine [UCLA], University of California at Los Angeles [Los Angeles] ( UCLA ) -School of Medicine, School of Earth and Environmental Sciences [Seoul] ( SEES ), Seoul National University [Seoul], Department of Chemistry, Seoul Women's University, MicroMachines Centre ( MMC ), Nanyang Technological University [Singapour], Regroupement Québécois sur les Matériaux de Pointe ( RQMP ), École Polytechnique de Montréal ( EPM ) -Université de Sherbrooke [Sherbrooke]-McGill University-Université de Montréal-Fonds Québécois de Recherche sur la Nature et les Technologies ( FQRNT ), Département de Physique [Montréal], Université de Montréal, School of Earth and Environment [Leeds] ( SEE ), Centre for Ecology and Hydrology ( CEH ), Natural Environment Research Council ( NERC ), Norwegian Institute for Water Research ( NIVA ), Norwegian Institute for Water Research, Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Astronomy Unit [London] (AU), Queen Mary University of London (QMUL), Commonwealth Scientific and Industrial Research Organisation Energy Technology (CSIRO Energy Technology), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Department of Biochemistry and Molecular Biology [Houston], The University of Texas Medical School at Houston, Mathematical Institute [Oxford] (MI), University of Oxford, Centre for the Analysis of Time Series (CATS), London School of Economics and Political Science (LSE), Thomas Jefferson National Accelerator Facility (Jefferson Lab), Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA ), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), University of Illinois System-University of Illinois System, Department of Electrical and Computer Engineering [Portland] (ECE), Portland State University [Portland] (PSU), Saint-Gobain, Institute for Animal Health (IAH), Biotechnology and Biological Sciences Research Council (BBSRC), Chinese Academy of Sciences [Changchun Branch] (CAS), Ipsen Inc. [Milford] (Ipsen), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Chung-Ang University (CAU), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Institute of Aerodynamics and Fluid Mechanics (AER), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Mer et santé (MS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), National Physical Laboratory [Teddington] (NPL), International Research Institute for Climate and Society (IRI), Macaulay Institute, University of Cambridge [UK] (CAM), Queen's University [Kingston, Canada], Leslie Hill Institute for Plant Conservation (PCU), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Interactive Systems Labs (ISL), Carnegie Mellon University [Pittsburgh] (CMU), Dalian Institute of Chemical Physics (DICP), Architectures, Languages and Compilers to Harness the End of Moore Years (ALCHEMY), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Clean Air Task Force (CATF), Indian Space Research Organisation (ISRO), Centre d'études et de recherches appliquées à la gestion (CERAG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS), Sultan Qaboos University (SQU)-College of Medicine and Health Sciences [Baylor], Baylor University-Baylor University, European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Michigan System-University of Michigan System, Department of Radiation Oncology [Michigan] (Radonc), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute for Meteorology and Climate Research (IMK), Karlsruhe Institute of Technology (KIT), University of New Brunswick (UNB), Laboratoire Parole et Langage (LPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Matériaux à Porosité Contrôlée (LMPC), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), School of Information Engineering [USTB] (SIE), University of Science and Technology Beijing [Beijing] (USTB), Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], School of Mathematics and Statistics [Sheffield] (SoMaS), Laboratoire de Mécanique de Lille - FRE 3723 (LML), Université de Lille, Sciences et Technologies-Centrale Lille-Centre National de la Recherche Scientifique (CNRS), Computer Science Department [UCLA] (CSD), University of California [Los Angeles] (UCLA), Développement et évolution (DE), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Pierre Aigrain (LPA), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Statistics [Montréal], McGill University = Université McGill [Montréal, Canada], Departamento de Botánica [Bariloche], Centro Regional Universitario Bariloche [Bariloche] (CRUB), Universidad Nacional del Comahue [Neuquén] (UNCOMA)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), Bioénergétique Cellulaire et Pathologique (BECP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratori Nazionali del Sud (LNS), Istituto Nazionale di Fisica Nucleare (INFN), Departament de Matemàtiques [Barcelona] (UAB), Universitat Autònoma de Barcelona (UAB), Max-Planck-Institut für Kohlenforschung (Coal Research), Max-Planck-Gesellschaft, CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS), National Chiao Tung University (NCTU), Department of Hydrology and Water Resources (HWR), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), University of Iowa [Iowa City], NASA Ames Research Center (ARC), Digital Language & Knowledge Contents Research Association (DICORA), Space Science and Technology Department [Didcot] (RAL Space), STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC)-Science and Technology Facilities Council (STFC), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), H M Nautical Almanac Office [RAL] (HMNAO), University College of London [London] (UCL), University of California (UC)-University of California (UC)-School of Medicine, School of Earth and Environmental Sciences [Seoul] (SEES), Seoul National University [Seoul] (SNU), MicroMachines Centre (MMC), Regroupement Québécois sur les Matériaux de Pointe (RQMP), École Polytechnique de Montréal (EPM)-Université de Sherbrooke (UdeS)-McGill University = Université McGill [Montréal, Canada]-Université de Montréal (UdeM)-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal (UdeM), Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Norwegian Institute for Water Research (NIVA), SEA URCHIN GENOME SEQUENCING CONSORTIUM, SODERGREN E, WEINSTOCK GM, DAVIDSON EH, CAMERON RA, GIBBS RA, ANGERER RC, ANGERER LM, ARNONE MI, BURGESS DR, BURKE RD, COFFMAN JA, DEAN M, ELPHICK MR, ETTENSOHN CA, FOLTZ KR, HAMDOUN A, HYNES RO, KLEIN WH, MARZLUFF W, MCCLAY DR, MORRIS RL, MUSHEGIAN A, RAST JP, SMITH LC, THORNDYKE MC, VACQUIER VD, WESSEL GM, WRAY G, ZHANG L, ELSIK CG, ERMOLAEVA O, HLAVINA W, HOFMANN G, KITTS P, LANDRUM MJ, MACKEY AJ, MAGLOTT D, PANOPOULOU G, POUSTKA AJ, PRUITT K, SAPOJNIKOV V, SONG X, SOUVOROV A, SOLOVYEV V, WEI Z, WHITTAKER CA, WORLEY K, DURBIN KJ, SHEN Y, FEDRIGO O, GARFIELD D, HAYGOOD R, PRIMUS A, SATIJA R, SEVERSON T, GONZALEZ-GARAY ML, JACKSON AR, MILOSAVLJEVIC A, TONG M, KILLIAN CE, LIVINGSTON BT, WILT FH, ADAMS N, BELLE R, CARBONNEAU S, CHEUNG R, CORMIER P, COSSON B, CROCE J, FERNANDEZ-GUERRA A, GENEVIERE AM, GOEL M, KELKAR H, MORALES J, MULNER-LORILLON O, ROBERTSON AJ, GOLDSTONE JV, COLE B, EPEL D, GOLD B, HAHN ME, HOWARD-ASHBY M, SCALLY M, STEGEMAN JJ, ALLGOOD EL, COOL J, JUDKINS KM, MCCAFFERTY SS, MUSANTE AM, OBAR RA, RAWSON AP, ROSSETTI BJ, GIBBONS IR, HOFFMAN MP, LEONE A, ISTRAIL S, MATERNA SC, SAMANTA MP, STOLC V, TONGPRASIT W, TU Q, BERGERON KF, BRANDHORST BP, WHITTLE J, BERNEY K, BOTTJER DJ, CALESTANI C, PETERSON K, CHOW E, YUAN QA, ELHAIK E, GRAUR D, REESE JT, BOSDET I, HEESUN S, MARRA MA, SCHEIN J, ANDERSON MK, BROCKTON V, BUCKLEY KM, COHEN AH, FUGMANN SD, HIBINO T, LOZA-COLL M, MAJESKE AJ, MESSIER C, NAIR SV, PANCER Z, TERWILLIGER DP, AGCA C, ARBOLEDA E, CHEN N, CHURCHER AM, HALLBOOK F, HUMPHREY GW, IDRIS MM, KIYAMA T, LIANG S, MELLOTT D, MU X, MURRAY G, OLINSKI RP, RAIBLE F, ROWE M, TAYLOR JS, TESSMAR-RAIBLE K, WANG D, WILSON KH, YAGUCHI S, GAASTERLAND T, GALINDO BE, GUNARATNE HJ, JULIANO C, KINUKAWA M, MOY GW, NEILL AT, NOMURA M, RAISCH M, READE A, ROUX MM, SONG JL, SU YH, TOWNLEY IK, VORONINA E, WONG JL, AMORE G, BRANNO M, BROWN ER, CAVALIERI, V, DUBOC V, DULOQUIN L, FLYTZANIS C, GACHE C, LAPRAZ F, LEPAGE T, LOCASCIO A, MART, University of California-University of California, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), University of California-University of California-School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), University of Manchester Institute of Science and Technology (UMIST), Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Brookhaven National Laboratory [Upton, NY] (BNL), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE), Baylor College of Medicine (BCM), Baylor University, Laboratoire de Traitement de l'Information Medicale (LaTIM), Université européenne de Bretagne - European University of Brittany (UEB)-Université de Brest (UBO)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire de Modélisation et Simulation Multi Echelle (MSME), Université Paris-Est Marne-la-Vallée (UPEM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Instituto Andaluz de Geofísica y Prevención de Desastres Sísmicos [Granada] (IAGPDS), Universidad de Granada (UGR), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), University of New South Wales [Sydney] (UNSW), Celera Genomics (CRA), Celera Genomics, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma Tor Vergata [Roma], Unité de recherches forestières (BORDX PIERR UR ), Institut National de la Recherche Agronomique (INRA), Deptartment of Neuroscience, Uppsala University, State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch]-Chinese Academy of Sciences [Nanjing Branch], Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), Department of Physical and Environmental Sciences [Toronto], University of Toronto at Scarborough, inconnu temporaire UPEMLV, Inconnu, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Atmospheric Sciences [Seattle], University of Washington [Seattle], National Institute of Advanced Industrial Science and Technology (AIST), Department of Pharmacy, Università degli studi di Genova = University of Genoa (UniGe), Interdisciplinary Arts and Sciences Department, St. Vincent's Hospital, Sydney, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Electrical Engineering (DEE-POSTECH), Pohang University of Science and Technology (POSTECH), Centre Suisse d'Electronique et de Microtechnique SA [Neuchatel] (CSEM), Centre Suisse d'Electronique et Microtechnique SA (CSEM), Human Genome Sequencing Center [Houston] (HGSC), Brookhaven National Laboratory, Meteorological Service of Canada, 4905 Dufferin Street, Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Mines-Télécom [Paris] (IMT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Paris-Est Marne-la-Vallée (UPEM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Forestières, Department of Physical and Environmental Sciences, University of Toronto [Scarborough, Canada], National Institute for Nuclear Physics (INFN), University of Genoa (UNIGE), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Universidad de Granada = University of Granada (UGR), Laboratoire d'Energétique et de Mécanique Théorique Appliquée (LEMTA ), Technische Universität München [München] (TUM), Queen's University [Kingston], Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Grenoble Alpes (UGA), Institut für Meteorologie und Klimaforschung (IMK), Karlsruher Institut für Technologie (KIT), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille, Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universitat Autònoma de Barcelona [Barcelona] (UAB), École Polytechnique de Montréal (EPM)-Université de Sherbrooke [Sherbrooke]-Université de Montréal [Montréal]-McGill University-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal [Montréal], U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, MESH: Signal Transduction, MESH: Sequence Analysis, DNA, MESH : Transcription Factors, MESH : Calcification, Physiologic, Genome, MESH : Proteins, 0302 clinical medicine, MESH : Embryonic Development, MESH: Gene Expression Regulation, Developmental, Innate, MESH: Embryonic Development, Developmental, Nervous System Physiological Phenomena, MESH: Animals, MESH: Proteins, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Complement Activation, ComputingMilieux_MISCELLANEOUS, MESH: Evolution, Molecular, MESH : Strongylocentrotus purpuratus, Genetics, 0303 health sciences, MESH: Nervous System Physiological Phenomena, Multidisciplinary, biology, Medicine (all), MESH: Immunologic Factors, Gene Expression Regulation, Developmental, Genome project, MESH: Transcription Factors, MESH : Immunity, Innate, MESH : Complement Activation, MESH: Genes, Bacterial artificial chromosome (BAC)DeuterostomesStrongylocentrotus purpuratusVertebrate innovations, Echinoderm, MESH : Nervous System Physiological Phenomena, embryonic structures, MESH: Cell Adhesion Molecules, MESH : Genes, MESH: Immunity, Innate, Sequence Analysis, Signal Transduction, MESH: Computational Biology, Genome evolution, MESH: Complement Activation, Sequence analysis, Evolution, MESH: Strongylocentrotus purpuratus, MESH : Male, Embryonic Development, MESH : Immunologic Factors, Article, MESH: Calcification, Physiologic, Calcification, MESH : Cell Adhesion Molecules, Evolution, Molecular, 03 medical and health sciences, Calcification, Physiologic, Animals, Immunologic Factors, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Physiologic, Gene, Strongylocentrotus purpuratus, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH : Signal Transduction, Bacterial artificial chromosome, Immunity, Molecular, Computational Biology, Proteins, Cell Adhesion Molecules, Genes, Immunity, Innate, Transcription Factors, Sequence Analysis, DNA, DNA, biology.organism_classification, MESH: Male, Gene Expression Regulation, MESH : Animals, MESH : Gene Expression Regulation, Developmental, MESH : Genome, 030217 neurology & neurosurgery, MESH : Computational Biology, MESH : Sequence Analysis, DNA
Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus , a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Published
2006

37. Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.

Author

Berrio A, Haygood R, and Wray GA

Subjects
Animals, Evolution, Molecular, Genetic Drift, Humans, Models, Genetic, Sequence Alignment, Sequence Analysis, DNA, Genome genetics, Genomics methods, Regulatory Sequences, Nucleic Acid genetics, Selection, Genetic
Abstract

Background: Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype., Results: We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We applied the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. Then, we evaluated the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity and specificity. We found that the length of the query alignment can vary between 150 bp and 1 kb without affecting the estimation of selection, while for the reference alignment, we found that a length of 3 kb is adequate for proper testing. We also simulated sequence alignments under different classes of evolution and validated our ability to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we re-confirmed that a quarter of all non-coding Human Accelerated Elements are evolving by positive selection., Conclusion: Here, we introduce a method we called adaptiPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome.

Published
2020
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38. Gene expression and adaptive noncoding changes during human evolution.

Author

Babbitt CC, Haygood R, Nielsen WJ, and Wray GA

Subjects
Animals, Gene Ontology, Genetic Variation, Genomics, Humans, Organ Specificity, Pan troglodytes genetics, RNA, Messenger genetics, Evolution, Molecular, Gene Expression Profiling, Genome, Human genetics, RNA, Untranslated genetics, Regulatory Sequences, Nucleic Acid genetics
Abstract

Background: Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear., Results: Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations., Conclusions: Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function.

Published
2017
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39. Spatio-Temporal Variation in Landscape Composition May Speed Resistance Evolution of Pests to Bt Crops.

Author

Ives AR, Paull C, Hulthen A, Downes S, Andow DA, Haygood R, Zalucki MP, and Schellhorn NA

Subjects
Animals, Bacterial Toxins genetics, Crops, Agricultural genetics, Ecosystem, Female, Larva, Male, Plants, Genetically Modified, Queensland, Spatio-Temporal Analysis, Agriculture methods, Bacillus thuringiensis, Biological Evolution, Gossypium genetics, Insecticide Resistance genetics, Moths genetics
Abstract

Transgenic crops that express insecticide genes from Bacillus thuringiensis (Bt) are used worldwide against moth and beetle pests. Because these engineered plants can kill over 95% of susceptible larvae, they can rapidly select for resistance. Here, we use a model for a pyramid two-toxin Bt crop to explore the consequences of spatio-temporal variation in the area of Bt crop and non-Bt refuge habitat. We show that variability over time in the proportion of suitable non-Bt breeding habitat, Q, or in the total area of Bt and suitable non-Bt habitat, K, can increase the overall rate of resistance evolution by causing short-term surges of intense selection. These surges can be exacerbated when temporal variation in Q and/or K cause high larval densities in refuges that increase density-dependent mortality; this will give resistant larvae in Bt fields a relative advantage over susceptible larvae that largely depend on refuges. We address the effects of spatio-temporal variation in a management setting for two bollworm pests of cotton, Helicoverpa armigera and H. punctigera, and field data on landscape crop distributions from Australia. Even a small proportion of Bt fields available to egg-laying females when refuges are sparse may result in high exposure to Bt for just a single generation per year and cause a surge in selection. Therefore, rapid resistance evolution can occur when Bt crops are rare rather than common in the landscape. These results highlight the need to understand spatio-temporal fluctuations in the landscape composition of Bt crops and non-Bt habitats in order to design effective resistance management strategies., Competing Interests: The authors have declared that no competing interests exist.

Published
2017
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40. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network.

Author

Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, and Wray GA

Subjects
Animals, Bone and Bones anatomy & histology, Gene Expression Profiling, Larva anatomy & histology, Larva genetics, Strongylocentrotus purpuratus growth & development, Biological Evolution, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Strongylocentrotus purpuratus genetics
Abstract

Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear), allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role., Competing Interests: The authors have declared that no competing interests exist.

Published
2013
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41. Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus.

Author

Garfield D, Haygood R, Nielsen WJ, and Wray GA

Subjects
Animals, Evolution, Molecular, Gene Expression Regulation, Developmental, Genetic Heterogeneity, Mutation, Polymorphism, Genetic, Strongylocentrotus purpuratus embryology, Genes, Developmental genetics, Regulatory Elements, Transcriptional genetics, Strongylocentrotus purpuratus genetics
Abstract

Despite the fact that noncoding sequences comprise a substantial fraction of functional sites within all genomes, the evolutionary mechanisms that operate on genetic variation within regulatory elements remain poorly understood. In this study, we examine the population genetics of the core, upstream cis-regulatory regions of eight genes (AN, CyIIa, CyIIIa, Endo16, FoxB, HE, SM30 a, and SM50) that function during the early development of the purple sea urchin, Strongylocentrotus purpuratus. Quantitative and qualitative measures of segregating variation are not conspicuously different between cis-regulatory and closely linked "proxy neutral" noncoding regions containing no known functional sites. Length and compound mutations are common in noncoding sequences; conventional descriptive statistics ignore such mutations, under-representing true genetic variation by approximately 28% for these loci in this population. Patterns of variation in the cis-regulatory regions of six of the genes examined (CyIIa, CyIIIa, Endo16, FoxB, AN, and HE) are consistent with directional selection. Genetic variation within annotated transcription factor binding sites is comparable to, and frequently greater than, that of surrounding sequences. Comparisons of two paralog pairs (CyIIa/CyIIIa and AN/HE) suggest that distinct evolutionary processes have operated on their cis-regulatory regions following gene duplication. Together, these analyses provide a detailed view of the evolutionary mechanisms operating on noncoding sequences within a natural population, and underscore how little is known about how these processes operate on cis-regulatory sequences., (© 2012 Wiley Periodicals, Inc.)

Published
2012
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42. A potential role for glucose transporters in the evolution of human brain size.

Author

Fedrigo O, Pfefferle AD, Babbitt CC, Haygood R, Wall CE, and Wray GA

Subjects
Animals, Base Sequence, Gene Expression, Glucose Transporter Type 4 genetics, Humans, Macaca, Molecular Sequence Data, Organ Size genetics, Pan troglodytes, Real-Time Polymerase Chain Reaction, Sodium-Phosphate Cotransporter Proteins, Type III genetics, Species Specificity, Biological Evolution, Brain anatomy & histology, Brain physiology, Glucose Transporter Type 4 biosynthesis, Sodium-Phosphate Cotransporter Proteins, Type III biosynthesis
Abstract

Differences in cognitive abilities and the relatively large brain are among the most striking differences between humans and their closest primate relatives. The energy trade-off hypothesis predicts that a major shift in energy allocation among tissues occurred during human origins in order to support the remarkable expansion of a metabolically expensive brain. However, the molecular basis of this adaptive scenario is unknown. Two glucose transporters (SLC2A1 and SLC2A4) are promising candidates and present intriguing mutations in humans, resulting, respectively, in microcephaly and disruptions in whole-body glucose homeostasis. We compared SLC2A1 and SLC2A4 expression between humans, chimpanzees and macaques, and found compensatory and biologically significant expression changes on the human lineage within cerebral cortex and skeletal muscle, consistent with mediating an energy trade-off. We also show that these two genes are likely to have undergone adaptation and participated in the development and maintenance of a larger brain in the human lineage by modulating brain and skeletal muscle energy allocation. We found that these two genes show human-specific signatures of positive selection on known regulatory elements within their 5'-untranslated region, suggesting an adaptation of their regulation during human origins. This study represents the first case where adaptive, functional and genetic lines of evidence implicate specific genes in the evolution of human brain size., (Copyright © 2011 S. Karger AG, Basel.)

Published
2011
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43. Contrasts between adaptive coding and noncoding changes during human evolution.

Author

Haygood R, Babbitt CC, Fedrigo O, and Wray GA

Subjects
Cognition physiology, Computational Biology, Gene Expression Profiling, Genomics methods, Humans, Models, Genetic, Nervous System Physiological Phenomena genetics, Adaptation, Biological genetics, Biological Evolution, Selection, Genetic, Untranslated Regions genetics
Abstract

Changes in non-protein-coding regulatory DNA sequences have been proposed to play distinctive roles in adaptive evolution. We analyzed correlations between gene functions and evidence for positive selection in a common statistical framework across several large surveys of coding and noncoding sequences throughout the human genome. Strong correlations with both classifications in gene ontologies and measurements of gene expression indicate that neural development and function have adapted mainly through noncoding changes. In contrast, adaptation via coding changes is dominated by immunity, olfaction, and male reproduction. Genes with highly tissue-specific expression have undergone more adaptive coding changes, suggesting that pleiotropic constraints inhibit such changes in broadly expressed genes. In contrast, adaptive noncoding changes do not exhibit this pattern. Our findings underscore the probable importance of noncoding changes in the evolution of human traits, particularly cognitive traits.

Published
2010
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44. Multiple Functional Variants in cis Modulate PDYN Expression.

Author

Babbitt CC, Silverman JS, Haygood R, Reininga JM, Rockman MV, and Wray GA

Subjects
Alleles, Binding Sites, Cell Line, Tumor, Genotype, Humans, Polymorphism, Genetic, Reverse Transcriptase Polymerase Chain Reaction, Enkephalins genetics, Genetic Variation, Protein Precursors genetics, Regulatory Sequences, Nucleic Acid genetics
Abstract

Understanding genetic variation and its functional consequences within cis-regulatory regions remains an important challenge in human genetics and evolution. Here, we present a fine-scale functional analysis of segregating variation within the cis-regulatory region of prodynorphin, a gene that encodes an endogenous opioid precursor with roles in cognition and disease. In order to characterize the functional consequences of segregating variation in cis in a region under balancing selection in different human populations, we examined associations between specific polymorphisms and gene expression in vivo and in vitro. We identified five polymorphisms within the 5' flanking region that affect transcript abundance: a 68-bp repeat recognized in prior studies, as well as two microsatellites and two single nucleotide polymorphisms not previously implicated as functional variants. The impact of these variants on transcription differs by brain region, sex, and cell type, implying interactions between cis genotype and the differentiated state of cells. The effects of individual variants on expression level are not additive in some combinations, implying epistatic interactions between nearby variants. These data reveal an unexpectedly complex relationship between segregating genetic variation and its expression-trait consequences and highlights the importance of close functional scrutiny of natural genetic variation within even relatively well-studied cis-regulatory regions.

Published
2010
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45. Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.

Author

Oliver TA, Garfield DA, Manier MK, Haygood R, Wray GA, and Palumbi SR

Subjects
Animals, Cell Communication, Comparative Genomic Hybridization, Evolution, Molecular, Female, Gene Expression, Life Cycle Stages, Male, Microarray Analysis, Models, Biological, Sequence Alignment, Ecosystem, Sea Urchins genetics, Selection, Genetic, Strongylocentrotus purpuratus genetics
Abstract

Comparisons of genomic sequence between divergent species can provide insight into the action of natural selection across many distinct classes of proteins. Here, we examine the extent of positive selection as a function of tissue-specific and stage-specific gene expression in two closely-related sea urchins, the shallow-water Strongylocentrotus purpuratus and the deep-sea Allocentrotus fragilis, which have diverged greatly in their adult but not larval habitats. Genes that are expressed specifically in adult somatic tissue have significantly higher dN/dS ratios than the genome-wide average, whereas those in larvae are indistinguishable from the genome-wide average. Testis-specific genes have the highest dN/dS values, whereas ovary-specific have the lowest. Branch-site models involving the outgroup S. franciscanus indicate greater selection (ω(FG)) along the A. fragilis branch than along the S. purpuratus branch. The A. fragilis branch also shows a higher proportion of genes under positive selection, including those involved in skeletal development, endocytosis, and sulfur metabolism. Both lineages are approximately equal in enrichment for positive selection of genes involved in immunity, development, and cell-cell communication. The branch-site models further suggest that adult-specific genes have experienced greater positive selection than those expressed in larvae and that ovary-specific genes are more conserved (i.e., experienced greater negative selection) than those expressed specifically in adult somatic tissues and testis. Our results chart the patterns of protein change that have occurred after habitat divergence in these two species and show that the developmental or functional context in which a gene acts can play an important role in how divergent species adapt to new environments.

Published
2010
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46. Functional consequences of genetic variation in primates on tyrosine hydroxylase (TH) expression in vitro.

Author

Warner LR, Babbitt CC, Primus AE, Severson TF, Haygood R, and Wray GA

Subjects
Analysis of Variance, Animals, Cell Line, Tumor, Cells, Cultured, Cloning, Molecular, Gorilla gorilla, Haplotypes, Humans, Macaca mulatta, Neurons physiology, Pan troglodytes, Polymorphism, Genetic genetics, Promoter Regions, Genetic genetics, Reverse Transcriptase Polymerase Chain Reaction, Transfection, Gene Expression Regulation, Enzymologic genetics, Genetic Variation genetics, Tyrosine 3-Monooxygenase genetics
Abstract

Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine synthesis, is known to contain naturally occurring genetic variation in it's promoter region that associates with a number of neuropsychological disorders. As such, examining non-coding regions is important for understanding tyrosine hydroxylase function in human health and disease. We examined approximately 2 kb upstream of the translation start site within humans and non-human primates to obtain a fine resolution map of evolutionarily and functionally relevant cis-regulatory differences. Our study investigated Macaca mulatta, Pan troglodytes, Gorilla gorilla, and Homo sapiens haplotypes using transient dual-luciferase transfection in three neuroblastoma cell lines to assay the impact of naturally occurring sequence variation on expression level. In addition to trans effects between cell lines, there are several significant expression differences between primate species, but the most striking difference was seen between human haplotypes in one cell line. Underlying this variation are numerous sequence polymorphisms, two of which influence expression within humans in a non-additive and cell line-specific manner. This study highlights functional consequences of tyrosine hydroxylase genetic variation in primates. Additionally, the results emphasize the importance of examining more than one cell line, the existence of multiple functional variants in a given promoter region and the presence of non-additive cis-interactions.

Published
2009
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47. Evolution of incompatibility-inducing microbes in subdivided host populations.

Author

Haygood R and Turelli M

Subjects
Animals, Extrachromosomal Inheritance, Female, Fertility, Insecta cytology, Male, Models, Biological, Models, Statistical, Sex Characteristics, Symbiosis, Biological Evolution, Insecta microbiology, Insecta physiology
Abstract

Many insects, other arthropods, and nematodes harbor maternally inherited bacteria inducing "cytoplasmic incompatibility" (CI), reduced egg hatch when infected males mate with uninfected females. Although CI drives the spread of these microbes, selection on alternative, mutually compatible strains in panmictic host populations does not act directly on CI intensity but favors higher "effective fecundity," the number of infected progeny an infected female produces. We analyze the consequences of host population subdivision using deterministic and stochastic models. In subdivided populations, effective fecundity remains the primary target of selection. For strains of equal effective fecundity, if population density is regulated locally (i.e., "soft selection"), variation among patches in infection frequencies may induce change in the relative frequencies of the strains. However, whether this change favors stronger incompatibility depends on initial frequencies. Demographic fluctuations maintain frequency variation that tends to favor stronger incompatibility. However, this effect is weak; even with small patches, minute increases in effective fecundity can offset substantial decreases in CI intensity. These results are insensitive to many details of host life cycle and migration and to systematic outbreeding or inbreeding within patches. Selection acting through transfer between host species may be required to explain the prevalence of CI.

Published
2009
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48. Evolutionary analysis of the cis-regulatory region of the spicule matrix gene SM50 in strongylocentrotid sea urchins.

Author

Walters J, Binkley E, Haygood R, and Romano LA

Subjects
Animals, Base Sequence, Cloning, Molecular, DNA genetics, DNA metabolism, DNA Primers genetics, Extracellular Matrix Proteins metabolism, Molecular Sequence Data, Phylogeny, Polymorphism, Genetic, Protein Binding, Sea Urchins classification, Sea Urchins metabolism, Selection, Genetic, Sequence Homology, Nucleic Acid, Species Specificity, Strongylocentrotus purpuratus classification, Strongylocentrotus purpuratus genetics, Strongylocentrotus purpuratus growth & development, Strongylocentrotus purpuratus metabolism, Evolution, Molecular, Extracellular Matrix Proteins genetics, Sea Urchins genetics, Sea Urchins growth & development
Abstract

An evolutionary analysis of transcriptional regulation is essential to understanding the molecular basis of phenotypic diversity. The sea urchin is an ideal system in which to explore the functional consequence of variation in cis-regulatory sequences. We are particularly interested in the evolution of genes involved in the patterning and synthesis of its larval skeleton. This study focuses on the cis-regulatory region of SM50, which has already been characterized to a considerable extent in the purple sea urchin, Strongylocentrotus purpuratus. We have isolated the cis-regulatory region from 15 individuals of S. purpuratus as well as seven closely related species in the family Strongylocentrotidae. We have performed a variety of statistical tests and present evidence that the cis-regulatory elements upstream of the SM50 gene have been subject to positive selection along the lineage leading to S. purpuratus. In addition, we have performed electrophoretic mobility shift assays (EMSAs) and demonstrate that nucleotide substitutions within Element C affect the ability of nuclear proteins to bind to this cis-regulatory element among members of the family Strongylocentrotidae. We speculate that such changes in SM50 and other genes could accumulate to produce altered patterns of gene expression with functional consequences during skeleton formation.

Published
2008
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49. When two is better than one.

Author

Babbitt CC, Haygood R, and Wray GA

Subjects
Adaptation, Physiological, Evolution, Molecular, Gene Duplication, Genetic Variation, Saccharomyces cerevisiae genetics
Abstract

Gene duplication and divergence has long been considered an important route to adaptation and phenotypic evolution. Reporting in Nature, Hittinger and Carroll (2007) provide the first clear example of adaptations in both regulatory regions and protein-coding regions after gene duplication. This combination of evolutionary changes appears to have resolved an adaptive conflict, leading to increased organismal fitness.

Published
2007
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50. Migration load and the coexistence of ecologically similar sexuals and asexuals.

Author

Spitzer BW and Haygood R

Subjects
Alleles, Animals, Population Dynamics, Selection, Genetic, Ecosystem, Models, Genetic, Reproduction genetics, Reproduction, Asexual genetics
Abstract

The frozen niche variation hypothesis suggests that sexuals can coexist with closely related, ecologically similar asexuals because sexuals and narrowly adapted asexual clones use different resources. However, because a collection of clones can potentially dominate the entire resource axis, such coexistence is not stable. We show that if the sexual population inhabits multiple selection regimes and asexuals are intrinsically slightly less fit than sexuals, migration load in the sexual population allows sexuals and asexuals to coexist stably at the regional level. By decreasing sexuals' fitness, migration load allows asexuals to invade the sexual population. However, as the sexuals' range contracts, migration load decreases, preventing asexuals from driving sexuals to extinction. This "buffering" effect of migration load is even more relevant in models that include more realistic conditions, such as demographic asymmetries or explicit spatial structure.

Published
2007
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