Back Matter
advertisement
Philosophical Transactions of the Royal Society B volume 368 2013 Published by THE ROYAL SOCIETY 6– 9 Carlton House Terrace, London SW1Y 5AG q 2013 The Royal Society ISSN 0962-8436 The twenty four numbers in this volume can be obtained separately from the Royal Society, 6 – 9 Carlton House Terrace, London SW1Y 5AG. Copyright q 2013 The Royal Society Except as otherwise permitted under the Copyright, Designs and Patents Act, 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission of the publisher, or, in the case of reprographic reproduction, in accordance with the terms of a licence issued by the copyright Licensing Agency. In particular, the Society permits the making of a single photocopy of an article from the issue (under Sections 29 and 38 of this Act) for an individual for the purposes of research or private study. The text paper used in this publication is alkaline sized with a coating which is predominantly calcium carbonate. The resultant surface pH is in excess of 7.5, which gives the maximum practical permanence. Printed in England by Latimer Trend & Company Limited Typeset in India by Techset Composition Limited Phil. Trans. R. Soc. B (2013) Contents Philosophical Transactions of the Royal Society B, Volume 368 no. 1609, 5 January 2013 Mammalian epigenetics in biology and medicine Papers of a Theme Issue compiled and edited by Fumitoshi Ishino, Yoichi Shinkai and Emma Whitelaw Introduction Mammalian epigenetics in biology and medicine By F. Ishino, Y. Shinkai and E. Whitelaw 20120386 Part I: Epigenetic aspects in mammalian development The origin and evolution of genomic imprinting and viviparity in mammals By M. B. Renfree, S. Suzuki and T. Kaneko-Ishino Importance of the matriline for genomic imprinting, brain development and behaviour By E. B. Keverne Advances in understanding chromosome silencing by the long non-coding RNA Xist By T. Sado and N. Brockdorff piRNA and spermatogenesis in mice By S. Chuma and T. Nakano Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs? By J. Sharif, Y. Shinkai and H. Koseki Part II: Molecular mechanisms working in the mammalian life cycle DNA methylation dynamics during the mammalian life cycle By J. A. Hackett and M. A. Surani Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers By S. Seisenberger, J. R. Peat, T. A. Hore, F. Santos, W. Dean and W. Reik New insights into establishment and maintenance of DNA methylation imprints in mammals By G. Kelsey and R. Feil Epigenetic inheritance mediated by histone lysine methylation: maintaining transcriptional states without the precise restoration of marks? By C. Huang, M. Xu and B. Zhu Part III: Epigenetics in reprogramming technologies, human health and medicine Recent advancements in cloning by somatic cell nuclear transfer By A. Ogura, K. Inoue and T. Wakayama Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier By A. Watanabe, Y. Yamada and S. Yamanaka Embryo manipulation via assisted reproductive technology and epigenetic asymmetry in mammalian early development By T. Kohda and F. Ishino Stem cell therapy: an exercise in patience and prudence By H.-T. Lin, M. Otsu and H. Nakauchi What obesity research tells us about epigenetic mechanisms By N. A. Youngson and M. J. Morris 20120151 20110327 20110325 20110338 20110340 20110328 20110330 20110336 20110332 20110329 20120292 20120353 20110334 20110337 no. 1610, 19 January 2013 Evolutionary rescue in changing environments Papers of a Theme Issue compiled and edited by Andrew Gonzalez, Ophélie Ronce, Regis Ferriere and Michael E. Hochberg Introduction Evolutionary rescue: an emerging focus at the intersection between ecology and evolution By A. Gonzalez, O. Ronce, R. Ferriere and M. E. Hochberg 20120404 Articles Evolutionary rescue and the limits of adaptation By G. Bell 20120080 Phil. Trans. R. Soc. B (2013) iii iv Contents The probability of evolutionary rescue: towards a quantitative comparison between theory and evolution experiments By G. Martin, R. Aguilée, J. Ramsayer, O. Kaltz and O. Ronce How competition affects evolutionary rescue By M. M. Osmond and C. de Mazancourt Evolutionary rescue by beneficial mutations in environments that change in space and time By M. Kirkpatrick and S. Peischl Limited evolutionary rescue of locally adapted populations facing climate change By K. Schiffers, E. C. Bourne, S. Lavergne, W. Thuiller and J. M. J. Travis Evolutionary and plastic rescue in multitrophic model communities By C. Kovach-Orr and G. F. Fussmann Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory By R. Ferriere and S. Legendre Evolutionary rescue and adaptation to abrupt environmental change depends upon the history of stress By A. Gonzalez and G. Bell Phenotypic plasticity in evolutionary rescue experiments By L.-M. Chevin, R. Gallet, R. Gomulkiewicz, R. D. Holt and S. Fellous Evolutionary rescue in vertebrates: evidence, applications and uncertainty By E. Vander Wal, D. Garant, M. Festa-Bianchet and F. Pelletier Predicting demographically sustainable rates of adaptation: can great tit breeding time keep pace with climate change? By P. Gienapp, M. Lof, T. E. Reed, J. McNamara, S. Verhulst and M. E. Visser Are species’ responses to global change predicted by past niche evolution? By S. Lavergne, M. E. K. Evans, I. J. Burfield, F. Jiguet and W. Thuiller What limits the evolutionary emergence of pathogens? By S. Gandon, M. E. Hochberg, R. D. Holt and T. Day Evolutionary rescue beyond the models By R. Gomulkiewicz and R. G. Shaw 20120088 20120085 20120082 20120083 20120084 20120081 20120079 20120089 20120090 20120289 20120091 20120086 20120093 no. 1611, 5 February 2013 Single molecule cellular biophysics: combining physics, biochemistry and cell biology to study the individual molecules of life Papers of a Theme Issue compiled and edited by Mark C. Leake Introduction The physics of life: one molecule at a time By M. C. Leake Articles Development of new photon-counting detectors for single-molecule fluorescence microscopy By X. Michalet, R. A. Colyer, G. Scalia, A. Ingargiola, R. Lin, J. E. Millaud, S. Weiss, O. H. W. Siegmund, A. S. Tremsin, J. V. Vallerga, A. Cheng, M. Levi, D. Aharoni, K. Arisaka, F. Villa, F. Guerrieri, F. Panzeri, I. Rech, A. Gulinatti, F. Zappa, M. Ghioni and S. Cova Reversible optical control of cyanine fluorescence in fixed and living cells: optical lock-in detection immunofluorescence imaging microscopy By Y. Yan, C. Petchprayoon, S. Mao and G. Marriott Single-molecule imaging in live bacteria cells By K. Ritchie, Y. Lill, C. Sood, H. Lee and S. Zhang A critical survey of methods to detect plasma membrane rafts By E. Klotzsch and G. J. Schütz Imaging the cell surface and its organization down to the level of single molecules By D. Klenerman, A. Shevchuk, P. Novak, Y. E. Korchev and S. J. Davis Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology By Y. Wang and J. Irudayaraj Towards physiological complexity with in vitro single-molecule biophysics By D. Duzdevich and E. C. Greene Twisting and subunit rotation in single FOF1-ATP synthase By H. Sielaff and M. Börsch High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase By T. Bilyard, M. Nakanishi-Matsui, B. C. Steel, T. Pilizota, A. L. Nord, H. Hosokawa, M. Futai and R. M. Berry Phil. Trans. R. Soc. B (2013) 20120248 20120035 20120031 20120355 20120033 20120027 20120026 20120271 20120024 20120023 Contents v Inferring diffusion in single live cells at the single-molecule level By A. Robson, K. Burrage and M. C. Leake High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking By G. Ullman, M. Wallden, E. G. Marklund, A. Mahmutovic, I. Razinkov and J. Elf 20120029 20120025 no. 1612, 19 February 2013 Cytochrome P450 and its impact on planet Earth Papers of a Theme Issue compiled and edited by David R. Nelson Introduction A world of cytochrome P450s By D. R. Nelson Articles Plant P450s as versatile drivers for evolution of species-specific chemical diversity By B. Hamberger and S. Bak Flower colour and cytochromes P450 By Y. Tanaka and F. Brugliera Origins of P450 diversity By H. Sezutsu, G. Le Goff and R. Feyereisen Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us? By S. L. Kelly and D. E. Kelly Unusual properties of the cytochrome P450 superfamily By D. C. Lamb and M. R. Waterman The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s By D. R. Nelson, J. V. Goldstone and J. J. Stegeman Role of cytochrome P450s in insecticide resistance: impact on the control of mosquito-borne diseases and use of insecticides on Earth By J.-P. David, H. M. Ismail, A. Chandor-Proust and M. J. I. Paine Human cytochromes P450 in health and disease By D. W. Nebert, K. Wikvall and W. L. Miller 20120430 20120426 20120432 20120428 20120476 20120434 20120474 20120429 20120431 no. 1613, 5 March 2013 The polyandry revolution Papers of a Theme Issue compiled and edited by Tommaso Pizzari and Nina Wedell Introduction The polyandry revolution By T. Pizzari and N. Wedell Articles Polyandry: the history of a revolution By G. A. Parker and T. R. Birkhead Polyandry as a mediator of sexual selection before and after mating By C. Kvarnemo and L. W. Simmons How multiple mating by females affects sexual selection By S. M. Shuster, W. R. Briggs and P. A. Dennis Polyandry and alternative mating tactics By B. D. Neff and E. I. Svensson Sexual networks: measuring sexual selection in structured, polyandrous populations By G. C. McDonald, R. James, J. Krause and T. Pizzari Sex allocation and investment into pre- and post-copulatory traits in simultaneous hermaphrodites: the role of polyandry and local sperm competition By L. Schärer and I. Pen The incidence and selection of multiple mating in plants By J. R. Pannell and A.-M. Labouche Selection on female remating interval is influenced by male sperm competition strategies and ejaculate characteristics By S. H. Alonzo and T. Pizzari Polyandry and sex-specific gene expression By J. E. Mank, N. Wedell and D. J. Hosken Phil. Trans. R. Soc. B (2013) 20120041 20120335 20120042 20120046 20120045 20120356 20120052 20120051 20120044 20120047 vi Contents Beyond promiscuity: mate-choice commitments in social breeding By J. J. Boomsma The dynamic relationship between polyandry and selfish genetic elements By N. Wedell Sexually transmitted infections in polygamous mating systems By B. Ashby and S. Gupta The consequences of polyandry for population viability, extinction risk and conservation By L. Holman and H. Kokko Corrections Correction to ‘To concentrate or ventilate? Carbon acquisition, isotope discrimination and physiological ecology of early land plant life forms’ By M. Meyer, U. Seibt and H. Griffiths 20120050 20120049 20120048 20120053 20120539 no. 1614, 19 March 2013 Next-generation molecular and evolutionary epidemiology of infectious disease Papers of a Discussion Meeting Issue compiled and edited by O. G. Pybus, C. Fraser and A. Rambaut Introduction Evolutionary epidemiology: preparing for an age of genomic plenty By O. G. Pybus, C. Fraser and A. Rambaut Articles Molecular evolutionary signatures reveal the role of host ecological dynamics in viral disease emergence and spread By S. M. Duke-Sylvester, R. Biek and L. A. Real Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission By C. Viboud, M. I. Nelson, Y. Tan and E. C. Holmes Coalescent inference for infectious disease: meta-analysis of hepatitis C By B. Dearlove and D. J. Wilson Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods By T. Stadler and S. Bonhoeffer Modelling tree shape and structure in viral phylodynamics By S. D. W. Frost and E. M. Volz The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis By H.-Y. Yuan and K. Koelle Multiple scales of selection influence the evolutionary emergence of novel pathogens By M. Park, C. Loverdo, S. J. Schreiber and J. O. Lloyd-Smith Graph hierarchies for phylogeography By G. B. Cybis, J. S. Sinsheimer, P. Lemey and M. A. Suchard Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin By A. G. Meyer, E. T. Dawson and C. O. Wilke The evolutionary dynamics of influenza A virus adaptation to mammalian hosts By S. Bhatt, T. T. Lam, S. J. Lycett, A. J. Leigh Brown, T. A. Bowden, E. C. Holmes, Y. Guan, J. L. N. Wood, I. H. Brown, P. Kellam, Combating Swine Influenza Consortium and O. G. Pybus The antigenic evolution of influenza: drift or thrift? By P. S. Wikramaratna, M. Sandeman, M. Recker and S. Gupta Global mapping of infectious disease By S. I. Hay, K. E. Battle, D. M. Pigott, D. L. Smith, C. L. Moyes, S. Bhatt, J. S. Brownstein, N. Collier, M. F. Myers, D. B. George and P. W. Gething Bacterial genomes in epidemiology—present and future By N. J. Croucher, S. R. Harris, Y. H. Grad and W. P. Hanage Viral population analysis and minority-variant detection using short read next-generation sequencing By S. J. Watson, M. R. A. Welkers, D. P. Depledge, E. Coulter, J. M. Breuer, M. D. de Jong and P. Kellam Observing micro-evolutionary processes of viral populations at multiple scales By R. J. Orton, C. F. Wright, M. J. Morelli, N. Juleff, G. Thébaud, N. J. Knowles, B. Valdazo-González, D. J. Paton, D. P. King and D. T. Haydon Phil. Trans. R. Soc. B (2013) 20120193 20120194 20120199 20120314 20120198 20120208 20120204 20120333 20120206 20120334 20120382 20120200 20120250 20120202 20120205 20120203 Contents Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints By N. R. Faria, M. A. Suchard, A. Rambaut, D. G. Streicker and P. Lemey Virulence attenuation during an influenza A/H5N1 pandemic By M. F. Boni, T. D. Nguyen, M. D. de Jong and H. R. van Doorn vii 20120196 20120207 no. 1615, 5 April 2013 The neurobiology of depression—revisiting the serotonin hypothesis. II. Genetic, epigenetic and clinical studies Papers of a Theme Issue compiled and edited by Laurent Descarries, Chawki Benkelfat and Paul R. Albert Introduction The neurobiology of depression—revisiting the serotonin hypothesis. II. Genetic, epigenetic and clinical studies By P. R. Albert and C. Benkelfat Articles Using the high-risk family design to identify biomarkers for major depression By A. Talati, M. M. Weissman and S. P. Hamilton Looking beyond the DNA sequence: the relevance of DNA methylation processes for the stress – diathesis model of depression By L. Booij, D. Wang, M. L. Lévesque, R. E. Tremblay and M. Szyf The serotonergic system in mood disorders and suicidal behaviour By J. J. Mann Genetics of impulsive behaviour By L. Bevilacqua and D. Goldman Anxiety and affective disorder comorbidity related to serotonin and other neurotransmitter systems: obsessive– compulsive disorder as an example of overlapping clinical and genetic heterogeneity By D. L. Murphy, P. R. Moya, M. A. Fox, L. M. Rubenstein, J. R. Wendland and K. R. Timpano Identifying serotonergic mechanisms underlying the corticolimbic response to threat in humans By P. M. Fisher and A. R. Hariri Imaging the serotonin 1A receptor using [11C]WAY100635 in healthy controls and major depression By N. Hesselgrave and R. V. Parsey Serotonin and beyond: therapeutics for major depression By P. Blier and M. El Mansari The effect of raising and lowering tryptophan levels on human mood and social behaviour By S. N. Young ‘It’s the way that you look at it’—a cognitive neuropsychological account of SSRI action in depression By C. J. Harmer and P. J. Cowen 20120535 20120129 20120251 20120537 20120380 20120435 20120192 20120004 20120536 20110375 20120407 no. 1616, 19 April 2013 Organohalide respiration: using halogenated hydrocarbons as the terminal electron acceptor Papers of a Theme Issue compiled and edited by David Leys, Lorenz Adrian and Hauke Smidt Introduction Organohalide respiration: microbes breathing chlorinated molecules By D. Leys, L. Adrian and H. Smidt Articles Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases By L. A. Hug, F. Maphosa, D. Leys, F. E. Löffler, H. Smidt, E. A. Edwards and L. Adrian The pentachlorophenol-dehalogenating Desulfitobacterium hafniense strain PCP-1 By R. Villemur Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone By T. Futagami, Y. Morono, T. Terada, A. H. Kaksonen and F. Inagaki Phil. Trans. R. Soc. B (2013) 20120316 20120322 20120319 20120249 viii Contents The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics By A. Rupakula, T. Kruse, S. Boeren, C. Holliger, H. Smidt and J. Maillard Organic cofactors in the metabolism of Dehalococcoides mccartyi strains By C. J. Schipp, E. Marco-Urrea, A. Kublik, J. Seifert and L. Adrian Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity By J. Yan, J. Im, Y. Yang and F. E. Löffler Identification of Dehalobacter reductive dehalogenases that catalyse dechlorination of chloroform, 1,1,1-trichloroethane and 1,1-dichloroethane By S. Tang and E. A. Edwards Identification of a reductive tetrachloroethene dehalogenase in Shewanella sediminis By S. T. Lohner and A. M. Spormann Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi By A. Wagner, L. Segler, S. Kleinsteuber, G. Sawers, H. Smidt and U. Lechner The transcriptional regulator CprK detects chlorination by combining direct and indirect readout mechanisms By L. R. Kemp, M. S. Dunstan, K. Fisher, J. Warwicker and D. Leys Why are chlorinated pollutants so difficult to degrade aerobically? Redox stress limits 1,3-dichloprop-1-ene metabolism by Pseudomonas pavonaceae By P. I. Nikel, D. Pérez-Pantoja and V. de Lorenzo 20120325 20120321 20120320 20120318 20120326 20120317 20120323 20120377 no. 1617, 5 May 2013 Assembly chaperones in health and disease Papers of a Theme Issue compiled and edited by Roy A. Quinlan and R. John Ellis Introduction Chaperones: needed for both the good times and the bad times By R. A. Quinlan and R. J. Ellis Articles Assembly chaperones: a perspective By R. J. Ellis Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2 By L.-Q. Xu, S. Wu, A. K. Buell, S. I. A. Cohen, L.-J. Chen, W.-H. Hu, S. A. Cusack, L. S. Itzhaki, H. Zhang, T. P. J. Knowles, C. M. Dobson, M. E. Welland, G. W. Jones and S. Perrett Ero1– PDI interactions, the response to redox flux and the implications for disulfide bond formation in the mammalian endoplasmic reticulum By A. M. Benham, M. van Lith, R. Sitia and I. Braakman Chaperone-like activity of the AAA+ proteins Rvb1 and Rvb2 in the assembly of various complexes By N. Nano and W. A. Houry Different anti-aggregation and pro-degradative functions of the members of the mammalian sHSP family in neurological disorders By S. Carra, P. Rusmini, V. Crippa, E. Giorgetti, A. Boncoraglio, R. Cristofani, M. Naujock, M. Meister, M. Minoia, H. H. Kampinga and A. Poletti Self-assembly of protein aggregates in ageing disorders: the lens and cataract model By J. I. Clark The specificity of the interaction between aB-crystallin and desmin filaments and its impact on filament aggregation and cell viability By J. L. Elliott, M. Der Perng, A. R. Prescott, K. A. Jansen, G. H. Koenderink and R. A. Quinlan Peptide aptamers: tools to negatively or positively modulate HSPB1(27) function By B. Gibert, S. Simon, V. Dimitrova, C. Diaz-Latoud and A.-P. Arrigo C-terminal interactions mediate the quaternary dynamics of aB-crystallin By G. R. Hilton, G. K. A. Hochberg, A. Laganowsky, S. I. McGinnigle, A. J. Baldwin and J. L. P. Benesch Changes in the quaternary structure and function of MjHSP16.5 attributable to deletion of the IXI motif and introduction of the substitution, R107G, in the a-crystallin domain By R. A. Quinlan, Y. Zhang, A. Lansbury, I. Williamson, E. Pohl and F. Sun Phil. Trans. R. Soc. B (2013) 20130091 20110398 20110410 20110403 20110399 20110409 20120104 20120375 20120075 20110405 20120327 Contents ix no. 1618, 19 May 2013 Flexibility and constraint in the evolution of mammalian social behaviour Papers of a Theme Issue compiled and edited by Peter M. Kappeler, Louise Barrett, Daniel T. Blumstein and Tim H. Clutton-Brock Introduction Constraints and flexibility in mammalian social behaviour: introduction and synthesis By P. M. Kappeler, L. Barrett, D. T. Blumstein and T. H. Clutton-Brock Articles Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors By C. Schradin Phylogenetic signal in primate behaviour, ecology and life history By J. M. Kamilar and N. Cooper Developmental constraints on behavioural flexibility By K. E. Holekamp, E. M. Swanson and P. E. Van Meter Behavioural profiles are shaped by social experience: when, how and why By N. Sachser, S. Kaiser and M. B. Hennessy Social environment influences the relationship between genotype and gene expression in wild baboons By D. E. Runcie, R. T. Wiedmann, E. A. Archie, J. Altmann, G. A. Wray, S. C. Alberts and J. Tung The costs and benefits of flexibility as an expression of behavioural plasticity: a primate perspective By C. P. van Schaik The interplay between social networks and culture: theoretically and among whales and dolphins By M. Cantor and H. Whitehead Scalar social dynamics in female vervet monkey cohorts By S. P. Henzi, N. Forshaw, R. Boner, L. Barrett and D. Lusseau Yellow-bellied marmots: insights from an emergent view of sociality By D. T. Blumstein Plasticity and constraints on social evolution in African mole-rats: ultimate and proximate factors By C. G. Faulkes and N. C. Bennett Identifying constraints in the evolution of primate societies By B. Thierry Variation in grouping patterns, mating systems and social structure: what socio-ecological models attempt to explain By A. Koenig, C. J. Scarry, B. C. Wheeler and C. Borries Social niche specialization under constraints: personality, social interactions and environmental heterogeneity By P.-O. Montiglio, C. Ferrari and D. Réale Taking note of Tinbergen, or: the promise of a biology of behaviour By L. Barrett, D. T. Blumstein, T. H. Clutton-Brock and P. M. Kappeler 20120337 20120346 20120341 20120350 20120344 20120345 20120339 20120340 20120351 20120349 20120347 20120342 20120348 20120343 20120352 no. 1619, 5 June 2013 Ecology, economy and management of an agroindustrial frontier landscape in the southeast Amazon Papers of a Theme Issue compiled and edited by Paulo M. Brando, Michael T. Coe and Ruth DeFries Introduction Ecology, economy and management of an agroindustrial frontier landscape in the southeast Amazon By P. M. Brando, M. T. Coe, R. DeFries and A. A. Azevedo 20120152 Articles Land-use-driven stream warming in southeastern Amazonia By M. N. Macedo, M. T. Coe, R. DeFries, M. Uriarte, P. M. Brando, C. Neill and W. S. Walker 20120153 Phil. Trans. R. Soc. B (2013) x Contents Watershed responses to Amazon soya bean cropland expansion and intensification By C. Neill, M. T. Coe, S. H. Riskin, A. V. Krusche, H. Elsenbeer, M. N. Macedo, R. McHorney, P. Lefebvre, E. A. Davidson, R. Scheffler, A. M. S. Figueira, S. Porder and L. A. Deegan The fate of phosphorus fertilizer in Amazon soya bean fields By S. H. Riskin, S. Porder, C. Neill, A. M. S. Figueira, C. Tubbesing and N. Mahowald Pesticide use and biodiversity conservation in the Amazonian agricultural frontier By L. Schiesari, A. Waichman, T. Brock, C. Adams and B. Grillitsch Ecological restoration of Xingu Basin headwaters: motivations, engagement, challenges and perspectives By G. Durigan, N. Guerin and J. N. M. N. da Costa Deforestation and climate feedbacks threaten the ecological integrity of south – southeastern Amazonia By M. T. Coe, T. R. Marthews, M. H. Costa, D. R. Galbraith, N. L. Greenglass, H. M. A. Imbuzeiro, N. M. Levine, Y. Malhi, P. R. Moorcroft, M. N. Muza, T. L. Powell, S. R. Saleska, L. A. Solorzano and J. Wang Understorey fire frequency and the fate of burned forests in southern Amazonia By D. C. Morton, Y. Le Page, R. DeFries, G. J. Collatz and G. C. Hurtt Effects of high-frequency understorey fires on woody plant regeneration in southeastern Amazonian forests By J. K. Balch, T. J. Massad, P. M. Brando, D. C. Nepstad and L. M. Curran Testing the Amazon savannization hypothesis: fire effects on invasion of a neotropical forest by native cerrado and exotic pasture grasses By D. V. Silvério, P. M. Brando, J. K. Balch, F. E. Putz, D. C. Nepstad, C. Oliveira-Santos and M. M. C. Bustamante Socioeconomic development and agricultural intensification in Mato Grosso By L. K. VanWey, S. Spera, R. de Sa, D. Mahr and J. F. Mustard The natural and social history of the indigenous lands and protected areas corridor of the Xingu River basin By S. Schwartzman, A. V. Boas, K. Y. Ono, M. G. Fonseca, J. Doblas, B. Zimmerman, P. Junqueira, A. Jerozolimski, M. Salazar, R. P. Junqueira and M. Torres A social and ecological assessment of tropical land uses at multiple scales: the Sustainable Amazon Network By T. A. Gardner, J. Ferreira, J. Barlow, A. C. Lees, L. Parry, I. C. G. Vieira, E. Berenguer, R. Abramovay, A. Aleixo, C. Andretti, L. E. O. C. Aragão, I. Araújo, W. S. de Ávila, R. D. Bardgett, M. Batistella, R. A. Begotti, T. Beldini, D. E. de Blas, R. F. Braga, D. de Lima Braga, J. G. de Brito, P. B. de Camargo, F. C. dos Santos, V. C. de Oliveira, A. C. N. Cordeiro, T. M. Cardoso, D. R. de Carvalho, S. A. Castelani, J. C. M. Chaul, C. E. Cerri, F. de Assis Costa, C. D. F. da Costa, E. Coudel, A. C. Coutinho, D. Cunha, Á. D’Antona, J. Dezincourt, K. Dias-Silva, M. Durigan, J. C. D. M. Esquerdo, J. Feres, S. F. de Barros Ferraz, A. E. de Melo Ferreira, A. C. Fiorini, L. V. F. da Silva, F. S. Frazão, R. Garrett, A. dos Santos Gomes, K. da Silva Gonçalves, J. B. Guerrero, N. Hamada, R. M. Hughes, D. C. Igliori, E. da Conceição Jesus, L. Juen, M. Junior, J. M. B. de Oliveira Junior, R. C. de Oliveira Junior, C. S. Junior, P. Kaufmann, V. Korasaki, C. G. Leal, R. Leitão, N. Lima, M. de Fátima Lopes Almeida, R. Lourival, J. Louzada, R. Mac Nally, S. Marchand, M. M. Maués, F. M. S. Moreira, C. Morsello, N. Moura, J. Nessimian, S. Nunes, V. H. F. Oliveira, R. Pardini, H. C. Pereira, P. S. Pompeu, C. R. Ribas, F. Rossetti, F. A. Schmidt, R. da Silva, R. C. V. M. da Silva, T. F. M. R. da Silva, J. Silveira, J. V. Siqueira, T. S. de Carvalho, R. R. C. Solar, N. S. H. Tancredi, J. R. Thomson, P. C. Torres, F. Z. Vaz-de-Mello, R. C. S. Veiga, A. Venturieri, C. Viana, D. Weinhold, R. Zanetti and J. Zuanon The DURAMAZ indicator system: a cross-disciplinary comparative tool for assessing ecological and social changes in the Amazon By F.-M. Le Tourneau, G. Marchand, A. Greissing, S. Nasuti, M. Droulers, M. Bursztyn, P. Léna and V. Dubreuil Responding to climate change and the global land crisis: REDD+, market transformation and low-emissions rural development By D. C. Nepstad, W. Boyd, C. M. Stickler, T. Bezerra and A. A. Azevedo Defending public interests in private lands: compliance, costs and potential environmental consequences of the Brazilian Forest Code in Mato Grosso By C. M. Stickler, D. C. Nepstad, A. A. Azevedo and D. G. McGrath Prospects for land-use sustainability on the agricultural frontier of the Brazilian Amazon By G. L. Galford, B. Soares-Filho and C. E. P. Cerri Export-oriented deforestation in Mato Grosso: harbinger or exception for other tropical forests? By R. DeFries, M. Herold, L. Verchot, M. N. Macedo and Y. Shimabukuro Phil. Trans. R. Soc. B (2013) 20120425 20120154 20120378 20120165 20120155 20120163 20120157 20120427 20120168 20120164 20120166 20120475 20120167 20120160 20120171 20120173 Contents xi no. 1620, 19 June 2013 Regulation from a distance: long-range regulation of gene expression Papers of a Discussion Meeting Issue organised and edited by Veronica van Heyningen and Wendy Bickmore Introduction Regulation from a distance: long-range control of gene expression in development and disease By V. van Heyningen and W. Bickmore Articles Alterations to the remote control of Shh gene expression cause congenital abnormalities By R. E. Hill and L. A. Lettice Chromatin organization and global regulation of Hox gene clusters By T. Montavon and D. Duboule High-resolution analysis of cis-acting regulatory networks at the a-globin locus By J. R. Hughes, K. M. Lower, I. Dunham, S. Taylor, M. De Gobbi, J. A. Sloane-Stanley, S. McGowan, J. Ragoussis, D. Vernimmen, R. J. Gibbons and D. R. Higgs Functional anatomy of distant-acting mammalian enhancers By D. E. Dickel, A. Visel and L. A. Pennacchio From remote enhancers to gene regulation: charting the genome’s regulatory landscapes By O. Symmons and F. Spitz CTCF: the protein, the binding partners, the binding sites and their chromatin loops By S. J. B. Holwerda and W. de Laat Deciphering cis-regulatory control in inflammatory cells By S. Ghisletti and G. Natoli Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts By C.-H. Hsu and I. Ovcharenko Human genetic variation within neural crest enhancers: molecular and phenotypic implications By A. Rada-Iglesias, S. L. Prescott and J. Wysocka Deconvoluting complex tissues for expression quantitative trait locus-based analyses By J.-H. Seo, Q. Li, A. Fatima, A. Eklund, Z. Szallasi, K. Polyak, A. L. Richardson and M. L. Freedman Expression quantitative trait loci: present and future By A. C. Nica and E. T. Dermitzakis 20120372 20120357 20120367 20120361 20120359 20120358 20120369 20120370 20120366 20120360 20120363 20120362 no. 1621, 5 July 2013 The global nitrogen cycle in the twenty-first century Papers of a Discussion Meeting Issue organised and edited by David Fowler, John A. Pyle, John A. Raven and Mark A. Sutton Introduction The global nitrogen cycle in the twenty-first century: introduction By D. Fowler, J. A. Pyle, J. A. Raven and M. A. Sutton Articles A chronology of human understanding of the nitrogen cycle By J. N. Galloway, A. M. Leach, A. Bleeker and J. W. Erisman Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems By P. M. Vitousek, D. N. L. Menge, S. C. Reed and C. C. Cleveland Processes regulating nitric oxide emissions from soils By K. Pilegaard Nitrous oxide emissions from soils: how well do we understand the processes and their controls? By K. Butterbach-Bahl, E. M. Baggs, M. Dannenmann, R. Kiese and S. Zechmeister-Boltenstern Global trends and uncertainties in terrestrial denitrification and N2O emissions By A. F. Bouwman, A. H. W. Beusen, J. Griffioen, J. W. Van Groenigen, M. M. Hefting, O. Oenema, P. J. T. M. Van Puijenbroek, S. Seitzinger, C. P. Slomp and E. Stehfest Towards a climate-dependent paradigm of ammonia emission and deposition By M. A. Sutton, S. Reis, S. N. Riddick, U. Dragosits, E. Nemitz, M. R. Theobald, Y. S. Tang, C. F. Braban, M. Vieno, A. J. Dore, R. F. Mitchell, S. Wanless, F. Daunt, D. Fowler, T. D. Blackall, C. Milford, C. R. Flechard, B. Loubet, R. Massad, P. Cellier, Phil. Trans. R. Soc. B (2013) 20130165 20130120 20130119 20130126 20130122 20130112 xii Contents E. Personne, P. F. Coheur, L. Clarisse, M. Van Damme, Y. Ngadi, C. Clerbaux, C. A. Skjøth, C. Geels, O. Hertel, R. J. Wichink Kruit, R. W. Pinder, J. O. Bash, J. T. Walker, D. Simpson, L. Horváth, T. H. Misselbrook, A. Bleeker, F. Dentener and W. de Vries The cycling of organic nitrogen through the atmosphere By T. Jickells, A. R. Baker, J. N. Cape, S. E. Cornell and E. Nemitz Sensitivity of continental United States atmospheric budgets of oxidized and reduced nitrogen to dry deposition parametrizations By R. L. Dennis, D. B. Schwede, J. O. Bash, J. E. Pleim, J. T. Walker and K. M. Foley The nitrogen cascade from agricultural soils to the sea: modelling nitrogen transfers at regional watershed and global scales By G. Billen, J. Garnier and L. Lassaletta The marine nitrogen cycle: recent discoveries, uncertainties and the potential relevance of climate change By M. Voss, H. W. Bange, J. W. Dippner, J. J. Middelburg, J. P. Montoya and B. Ward Ice sheets and nitrogen By E. W. Wolff Terrestrial nitrogen – carbon cycle interactions at the global scale By S. Zaehle Consequences of human modification of the global nitrogen cycle By J. W. Erisman, J. N. Galloway, S. Seitzinger, A. Bleeker, N. B. Dise, A. M. R. Petrescu, A. M. Leach and W. de Vries The global nitrogen cycle in the twenty-first century By D. Fowler, M. Coyle, U. Skiba, M. A. Sutton, J. N. Cape, S. Reis, L. J. Sheppard, A. Jenkins, B. Grizzetti, J. N. Galloway, P. Vitousek, A. Leach, A. F. Bouwman, K. Butterbach-Bahl, F. Dentener, D. Stevenson, M. Amann and M. Voss 20130166 20130115 20130124 20130123 20130121 20130127 20130125 20130116 20130164 no. 1622, 19 July 2013 Energy transduction and genome function: an evolutionary synthesis Papers of a Discussion Meeting Issue organised and edited by Nick Lane, William F. Martin, John A. Raven, John F. Allen Introduction Energy, genes and evolution: introduction to an evolutionary synthesis By N. Lane, W. F. Martin, J. A. Raven and J. F. Allen Articles The energetics of organic synthesis inside and outside the cell By J. P. Amend, D. E. LaRowe, T. M. McCollom and E. L. Shock The inevitable journey to being By M. J. Russell, W. Nitschke and E. Branscomb Beating the acetyl coenzyme A-pathway to the origin of life By W. Nitschke and M. J. Russell Early bioenergetic evolution By F. L. Sousa, T. Thiergart, G. Landan, S. Nelson-Sathi, I. A. C. Pereira, J. F. Allen, N. Lane and W. F. Martin Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases By J. D. Kim, S. Senn, A. Harel, B. I. Jelen and P. G. Falkowski Energy, ecology and the distribution of microbial life By J. L. Macalady, T. L. Hamilton, C. L. Grettenberger, D. S. Jones, L. E. Tsao and W. D. Burgos Controlling the delicate balance of tetrapyrrole biosynthesis By L. Yin and C. E. Bauer Interactions of photosynthesis with genome size and function By J. A. Raven, J. Beardall, A. W. D. Larkum and P. Sánchez-Baracaldo Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation By N. W. Blackstone Requirements of the cytosolic iron– sulfur cluster assembly pathway in Arabidopsis By D. G. Bernard, D. J. A. Netz, T. J. Lagny, A. J. Pierik and J. Balk Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts By S. Puthiyaveetil, I. M. Ibrahim and J. F. Allen Phil. Trans. R. Soc. B (2013) 20120253 20120255 20120254 20120258 20130088 20120257 20120383 20120262 20120264 20120266 20120259 20120260 Contents Energy, ageing, fidelity and sex: oocyte mitochondrial DNA as a protected genetic template By W. B. M. de Paula, C. H. Lucas, A.-N. A. Agip, G. Vizcay-Barrena and J. F. Allen Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases By D. C. Wallace xiii 20120263 20120267 no. 1623, 5 August 2013 Towards the endgame and beyond: complexities and challenges for the elimination of infectious diseases Papers of a Theme Issue compiled and edited by Petra Klepac, C. Jessica E. Metcalf and Katie Hampson Introduction Towards the endgame and beyond: complexities and challenges for the elimination of infectious diseases By P. Klepac, C. J. E. Metcalf, A. R. McLean and K. Hampson Articles Lessons from the eradication of smallpox: an interview with D. A. Henderson By D. A. Henderson and P. Klepac Rinderpest: the veterinary perspective on eradication By P. Roeder, J. Mariner and R. Kock The final stages of the global eradication of poliomyelitis By N. C. Grassly Think globally, act locally: the role of local demographics and vaccination coverage in the dynamic response of measles infection to control By M. J. Ferrari, B. T. Grenfell and P. M. Strebel The elimination of fox rabies from Europe: determinants of success and lessons for the future By C. M. Freuling, K. Hampson, T. Selhorst, R. Schröder, F. X. Meslin, T. C. Mettenleiter and T. Müller Progress towards eliminating canine rabies: policies and perspectives from Latin America and the Caribbean By M. A. N. Vigilato, A. Clavijo, T. Knobl, H. M. T. Silva, O. Cosivi, M. C. Schneider, L. F. Leanes, A. J. Belotto and M. A. Espinal Elimination of foot-and-mouth disease in South America: lessons and challenges By J. Naranjo and O. Cosivi Dracunculiasis (guinea worm disease): eradication without a drug or a vaccine By G. Biswas, D. P. Sankara, J. Agua-Agum and A. Maiga Preventive chemotherapy as a strategy for elimination of neglected tropical parasitic diseases: endgame challenges By M. J. Bockarie, L. A. Kelly-Hope, M. Rebollo and D. H. Molyneux A sticky situation: the unexpected stability of malaria elimination By D. L. Smith, J. M. Cohen, C. Chiyaka, G. Johnston, P. W. Gething, R. Gosling, C. O. Buckee, R. Laxminarayan, S. I. Hay and A. J. Tatem The impact of protein-conjugate polysaccharide vaccines: an endgame for meningitis? By M. C. J. Maiden Vaccine refusal and the endgame: walking the last mile first By D. S. Saint-Victor and S. B. Omer Economic considerations for the eradication endgame By S. Barrett Vacated niches, competitive release and the community ecology of pathogen eradication By J. O. Lloyd-Smith 20120137 20130113 20120139 20120140 20120141 20120142 20120143 20120381 20120146 20120144 20120145 20120147 20120148 20120149 20120150 no. 1624, 19 August 2013 Long-term changes in Arctic tundra ecosystems Papers of a Theme Issue compiled and edited by Eric Post and Toke T. Høye Introduction Advancing the long view of ecological change in tundra systems By E. Post and T. T. Høye Phil. Trans. R. Soc. B (2013) 20120477 xiv Contents Articles Nonlinear flowering responses to climate: are species approaching their limits of phenological change? By A. M. Iler, T. T. Høye, D. W. Inouye and N. M. Schmidt Phenological response of tundra plants to background climate variation tested using the International Tundra Experiment By S. F. Oberbauer, S. C. Elmendorf, T. G. Troxler, R. D. Hollister, A. V. Rocha, M. S. Bret-Harte, M. A. Dawes, A. M. Fosaa, G. H. R. Henry, T. T. Høye, F. C. Jarrad, I. S. Jónsdóttir, K. Klanderud, J. A. Klein, U. Molau, C. Rixen, N. M. Schmidt, G. R. Shaver, R. T. Slider, Ø. Totland, C.-H. Wahren and J. M. Welker Complex biotic interactions drive long-term vegetation dynamics in a subarctic ecosystem By J. Olofsson, M. te Beest and L. Ericson Long-term monitoring at multiple trophic levels suggests heterogeneity in responses to climate change in the Canadian Arctic tundra By G. Gauthier, J. Bêty, M.-C. Cadieux, P. Legagneux, M. Doiron, C. Chevallier, S. Lai, A. Tarroux and D. Berteaux Capital and income breeding traits differentiate trophic match – mismatch dynamics in large herbivores By J. Kerby and E. Post Changing seasonality and phenological responses of free-living male arctic ground squirrels: the importance of sex By M. J. Sheriff, M. M. Richter, C. L. Buck and B. M. Barnes Ecosystem change and stability over multiple decades in the Swedish subarctic: complex processes and multiple drivers By T. V. Callaghan, C. Jonasson, T. Thierfelder, Z. Yang, H. Hedenås, M. Johansson, U. Molau, R. Van Bogaert, A. Michelsen, J. Olofsson, D. Gwynn-Jones, S. Bokhorst, G. Phoenix, J. W. Bjerke, H. Tømmervik, T. R. Christensen, E. Hanna, E. K. Koller and V. L. Sloan A greener Greenland? Climatic potential and long-term constraints on future expansions of trees and shrubs By S. Normand, C. Randin, R. Ohlemüller, C. Bay, T. T. Høye, E. D. Kjær, C. Körner, H. Lischke, L. Maiorano, J. Paulsen, P. B. Pearman, A. Psomas, U. A. Treier, N. E. Zimmermann and J.-C. Svenning Pan-Arctic modelling of net ecosystem exchange of CO2 By G. R. Shaver, E. B. Rastetter, V. Salmon, L. E. Street, M. J. van de Weg, A. Rocha, M. T. van Wijk and M. Williams The response of Arctic vegetation and soils following an unusually severe tundra fire By M. S. Bret-Harte, M. C. Mack, G. R. Shaver, D. C. Huebner, M. Johnston, C. A. Mojica, C. Pizano and J. A. Reiskind Corrections A social and ecological assessment of tropical land uses at multiple scales: the Sustainable Amazon Network By T. A. Gardner, J. Ferreira, J. Barlow, A. C. Lees, L. Parry, I. C. G. Vieira, E. Berenguer, R. Abramovay, A. Aleixo, C. Andretti, L. E. O. C. Aragão, I. Araújo, W. S. de Ávila, R. D. Bardgett, M. Batistella, R. A. Begotti, T. Beldini, D. E. de Blas, R. F. Braga, D. de Lima Braga, J. G. de Brito, P. B. de Camargo, F. C. dos Santos, V. C. de Oliveira, A. C. N. Cordeiro, T. M. Cardoso, D. R. de Carvalho, S. A. Castelani, J. C. M. Chaul, C. E. Cerri, F. de Assis Costa, C. D. F. da Costa, E. Coudel, A. C. Coutinho, D. Cunha, Á. D’Antona, J. Dezincourt, K. Dias-Silva, M. Durigan, J. C. D. M. Esquerdo, J. Feres, S. F. de Barros Ferraz, A. E. de Melo Ferreira, A. C. Fiorini, L. V. F. da Silva, F. S. Frazão, R. Garrett, A. dos Santos Gomes, K. da Silva Gonçalves, J. B. Guerrero, N. Hamada, R. M. Hughes, D. C. Igliori, E. da Conceição Jesus, L. Juen, M. Junior, J. M. B. de Oliveira Junior, R. C. de Oliveira Junior, C. S. Junior, P. Kaufmann, V. Korasaki, C. G. Leal, R. Leitão, N. Lima, M. de Fátima Lopes Almeida, R. Lourival, J. Louzada, R. M. Nally, S. Marchand, M. M. Maués, F. M. S. Moreira, C. Morsello, N. Moura, J. Nessimian, S. Nunes, V. H. F. Oliveira, R. Pardini, H. C. Pereira, P. S. Pompeu, C. R. Ribas, F. Rossetti, F. A. Schmidt, R. da Silva, R. C. V. M. da Silva, T. F. M. R. da Silva, J. Silveira, J. V. Siqueira, T. S. de Carvalho, R. R. C. Solar, N. S. H. Tancredi, J. R. Thomson, P. C. Torres, F. Z. Vaz-de-Mello, R. C. S. Veiga, A. Venturieri, C. Viana, D. Weinhold, R. Zanetti and J. Zuanon Phil. Trans. R. Soc. B (2013) 20120489 20120481 20120486 20120482 20120484 20120480 20120488 20120479 20120485 20120490 20130307 Contents The natural and social history of the indigenous lands and protected areas corridor of the Xingu River basin By S. Schwartzman, A. V. Boas, K. Y. Ono, M. G. Fonseca, J. Doblas, B. Zimmerman, P. Junqueira, A. Jerozolimski, M. Salazar, R. P. Junqueira and M. Torres xv 20130308 no. 1625, 5 September 2013 Change in African rainforests: past, present and future Papers of a Theme Issue compiled and edited by Yadvinder Malhi, Stephen Adu-Bredu, Rebecca Asare, Simon Lewis and Philippe Mayaux Introduction The past, present and future of Africa’s rainforests By Y. Malhi, S. Adu-Bredu, R. A. Asare, S. L. Lewis and P. Mayaux Articles State and evolution of the African rainforests between 1990 and 2010 By P. Mayaux, J.-F. Pekel, B. Desclée, F. Donnay, A. Lupi, F. Achard, M. Clerici, C. Bodart, A. Brink, R. Nasi and A. Belward The national determinants of deforestation in sub-Saharan Africa By T. K. Rudel Above-ground biomass and structure of 260 African tropical forests By S. L. Lewis, B. Sonké, T. Sunderland, S. K. Begne, G. Lopez-Gonzalez, G. M. F. van der Heijden, O. L. Phillips, K. Affum-Baffoe, T. R. Baker, L. Banin, J.-F. Bastin, H. Beeckman, P. Boeckx, J. Bogaert, C. De Cannière, E. Chezeaux, C. J. Clark, M. Collins, G. Djagbletey, M. N. K. Djuikouo, V. Droissart, J.-L. Doucet, C. E. N. Ewango, S. Fauset, T. R. Feldpausch, E. G. Foli, J.-F. Gillet, A. C. Hamilton, D. J. Harris, T. B. Hart, T. de Haulleville, A. Hladik, K. Hufkens, D. Huygens, P. Jeanmart, K. J. Jeffery, E. Kearsley, M. E. Leal, J. Lloyd, J. C. Lovett, J.-R. Makana, Y. Malhi, A. R. Marshall, L. Ojo, K. S.-H. Peh, G. Pickavance, J. R. Poulsen, J. M. Reitsma, D. Sheil, M. Simo, K. Steppe, H. E. Taedoumg, J. Talbot, J. R. D. Taplin, D. Taylor, S. C. Thomas, B. Toirambe, H. Verbeeck, J. Vleminckx, L. J. T. White, S. Willcock, H. Woell and L. Zemagho Climatic and cultural changes in the west Congo Basin forests over the past 5000 years By R. Oslisly, L. White, I. Bentaleb, C. Favier, M. Fontugne, J.-F. Gillet and D. Sebag Determining the response of African biota to climate change: using the past to model the future By K. J. Willis, K. D. Bennett, S. L. Burrough, M. Macias-Fauria and C. Tovar Extent and ecological consequences of hunting in Central African rainforests in the twenty-first century By K. A. Abernethy, L. Coad, G. Taylor, M. E. Lee and F. Maisels Woody encroachment and forest degradation in sub-Saharan Africa’s woodlands and savannas 1982 – 2006 By E. T. A. Mitchard and C. M. Flintrop Tropical forest recovery from logging: a 24 year silvicultural experiment from Central Africa By S. Gourlet-Fleury, F. Mortier, A. Fayolle, F. Baya, D. Ouédraogo, F. Bénédet and N. Picard Vegetation structure and greenness in Central Africa from Modis multi-temporal data By V. Gond, A. Fayolle, A. Pennec, G. Cornu, P. Mayaux, P. Camberlin, C. Doumenge, N. Fauvet and S. Gourlet-Fleury African tropical rainforest net carbon dioxide fluxes in the twentieth century By J. B. Fisher, M. Sikka, S. Sitch, P. Ciais, B. Poulter, D. Galbraith, J.-E. Lee, C. Huntingford, N. Viovy, N. Zeng, A. Ahlström, M. R. Lomas, P. E. Levy, C. Frankenberg, S. Saatchi and Y. Malhi Implications of global warming for the climate of African rainforests By R. James, R. Washington and D. P. Rowell Congo Basin rainfall climatology: can we believe the climate models? By R. Washington, R. James, H. Pearce, W. M. Pokam and W. Moufouma-Okia Attribution of changes in precipitation patterns in African rainforests By F. E. L. Otto, R. G. Jones, K. Halladay and M. R. Allen Response of African humid tropical forests to recent rainfall anomalies By S. Asefi-Najafabady and S. Saatchi Financing and current capacity for REDD+ readiness and monitoring, measurement, reporting and verification in the Congo Basin By D. Maniatis, J. Gaugris, D. Mollicone, J. Scriven, A. Corblin, C. Ndikumagenge, A. Aquino, P. Crete and M.-J. Sanz-Sanchez Phil. Trans. R. Soc. B (2013) 20120293 20120300 20120405 20120295 20120304 20120491 20120303 20120406 20120302 20120309 20120376 20120298 20120296 20120299 20120306 20120310 xvi Contents The community resource management area mechanism: a strategy to manage African forest resources for REDD+ By R. A. Asare, A. Kyei and J. J. Mason African rainforests: past, present and future By Y. Malhi, S. Adu-Bredu, R. A. Asare, S. L. Lewis and P. Mayaux 20120311 20120312 no. 1626, 19 September 2013 Paleovirology: insights from the genomic fossil record Papers of a Theme Issue compiled and edited by Aris Katzourakis Introduction Paleovirology: inferring viral evolution from host genome sequence data By A. Katzourakis Articles On the concept and elucidation of endogenous retroviruses By R. A. Weiss Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals By A. Lee, A. Nolan, J. Watson and M. Tristem Pushing the endogenous envelope By J. E. Henzy and W. E. Johnson Host gene evolution traces the evolutionary history of ancient primate lentiviruses By A. A. Compton, H. S. Malik and M. Emerman Apparent effect of rabbit endogenous lentivirus type K acquisition on retrovirus restriction by lagomorph Trim5as By M. W. Yap and J. P. Stoye ‘There and back again’: revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era By G. Magiorkinis, R. Belshaw and A. Katzourakis Paleovirology of ‘syncytins’, retroviral env genes exapted for a role in placentation By C. Lavialle, G. Cornelis, A. Dupressoir, C. Esnault, O. Heidmann, C. Vernochet and T. Heidmann When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses By E. A. Herniou, E. Huguet, J. Thézé, A. Bézier, G. Periquet and J.-M. Drezen Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses By A. Bézier, F. Louis, S. Jancek, G. Periquet, J. Thézé, G. Gyapay, K. Musset, J. Lesobre, P. Lenoble, C. Dupuy, D. Gundersen-Rindal, E. A. Herniou and J.-M. Drezen Exploring the effects of immunity and life history on the dynamics of an endogenous retrovirus By R. K. Kanda, M. Tristem and T. Coulson Evolutionary analysis of hepatitis C virus gene sequences from 1953 By R. R. Gray, Y. Tanaka, Y. Takebe, G. Magiorkinis, Z. Buskell, L. Seeff, H. J. Alter and O. G. Pybus Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes By M. Horie, Y. Kobayashi, Y. Suzuki and K. Tomonaga Corrections Financing and current capacity for REDD+ readiness and monitoring, measurement, reporting and verification in the Congo Basin By D. Maniatis, J. Gaugris, D. Mollicone, J. Scriven, A. Corblin, C. Ndikumagenge, A. Aquino, P. Crete and M.-J. Sanz-Sanchez 20120493 20120494 20120503 20120506 20120496 20120498 20120504 20120507 20130051 20130047 20120505 20130168 20120499 20130413 no. 1627, 5 October 2013 Ocean acidification and climate change: advances in ecology and evolution Papers of a Theme Issue compiled and edited by Jasmin A. Godbold and Piero Calosi Introduction Ocean acidification and climate change: advances in ecology and evolution By J. A. Godbold and P. Calosi Phil. Trans. R. Soc. B (2013) 20120448 Contents xvii Articles The other ocean acidification problem: CO2 as a resource among competitors for ecosystem dominance By S. D. Connell, K. J. Kroeker, K. E. Fabricius, D. I. Kline and B. D. Russell Ocean acidification and rising temperatures may increase biofilm primary productivity but decrease grazer consumption By B. D. Russell, S. D. Connell, H. S. Findlay, K. Tait, S. Widdicombe and N. Mieszkowska Long-term effects of warming and ocean acidification are modified by seasonal variation in species responses and environmental conditions By J. A. Godbold and M. Solan Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification By B. Laverock, V. Kitidis, K. Tait, J. A. Gilbert, A. M. Osborn and S. Widdicombe Effects of acidification on olfactory-mediated behaviour in freshwater and marine ecosystems: a synthesis By A. O. H. C. Leduc, P. L. Munday, G. E. Brown and M. C. O. Ferrari The stunting effect of a high CO2 ocean on calcification and development in sea urchin larvae, a synthesis from the tropics to the poles By M. Byrne, M. Lamare, D. Winter, S. A. Dworjanyn and S. Uthicke Adaptation and acclimatization to ocean acidification in marine ectotherms: an in situ transplant experiment with polychaetes at a shallow CO2 vent system By P. Calosi, S. P. S. Rastrick, C. Lombardi, H. J. de Guzman, L. Davidson, M. Jahnke, A. Giangrande, J. D. Hardege, A. Schulze, J. I. Spicer and M.-C. Gambi Emiliania huxleyi increases calcification but not expression of calcification-related genes in long-term exposure to elevated temperature and pCO2 By I. Benner, R. E. Diner, S. C. Lefebvre, D. Li, T. Komada, E. J. Carpenter and J. H. Stillman Short- and long-term conditioning of a temperate marine diatom community to acidification and warming By A. O. Tatters, M. Y. Roleda, A. Schnetzer, F. Fu, C. L. Hurd, P. W. Boyd, D. A. Caron, A. A. Y. Lie, L. J. Hoffmann and D. A. Hutchins Corrections Controlling the delicate balance of tetrapyrrole biosynthesis By L. Yin and C. E. Bauer 20120442 20120438 20130186 20120441 20120447 20120439 20120444 20130049 20120437 20130416 no. 1628, 19 October 2013 Attentional selection in visual perception, memory and action Papers of a Theme Issue compiled and edited by Werner X. Schneider, Wolfgang Einhäuser and Gernot Horstmann Introduction Attentional selection in visual perception, memory and action: a quest for cross-domain integration By W. X. Schneider, W. Einhäuser and G. Horstmann Articles Attending to the possibilities of action By G. W. Humphreys, S. Kumar, E. Y. Yoon, M. Wulff, K. L. Roberts and M. J. Riddoch The role of observers’ gaze behaviour when watching object manipulation tasks: predicting and evaluating the consequences of action By J. R. Flanagan, G. Rotman, A. F. Reichelt and R. S. Johansson Reach preparation enhances visual performance and appearance By M. Rolfs, B. M. Lawrence and M. Carrasco Feature-based attention: it is all bottom-up priming By J. Theeuwes Temporal expectancy in the context of a theory of visual attention By S. Vangkilde, A. Petersen and C. Bundesen A biased competition account of attention and memory in Alzheimer’s disease By K. Finke, N. Myers, P. Bublak and C. Sorg Selective visual processing across competition episodes: a theory of task-driven visual attention and working memory By W. X. Schneider Phil. Trans. R. Soc. B (2013) 20130053 20130059 20130063 20130057 20130055 20130054 20130062 20130060 xviii Contents The relationship between visual working memory and attention: retention of precise colour information in the absence of effects on perceptual selection By A. Hollingworth and S. Hwang Modelling eye movements in a categorical search task By G. J. Zelinsky, H. Adeli, Y. Peng and D. Samaras Attention in natural scenes: contrast affects rapid visual processing and fixations alike By B. M. ’t Hart, H. C. E. F. Schmidt, I. Klein-Harmeyer and W. Einhäuser Priorities for selection and representation in natural tasks By B. W. Tatler, Y. Hirose, S. K. Finnegan, R. Pievilainen, C. Kirtley and A. Kennedy Memory and prediction in natural gaze control By G. Diaz, J. Cooper and M. Hayhoe Selection of visual information for lightness judgements by eye movements By M. Toscani, M. Valsecchi and K. R. Gegenfurtner Evidence for differential top-down and bottom-up suppression in posterior parietal cortex By K. Mirpour and J. W. Bisley Control of the superior colliculus by the lateral prefrontal cortex By S. Everling and K. Johnston Neural chronometry and coherency across speed – accuracy demands reveal lack of homomorphism between computational and neural mechanisms of evidence accumulation By R. P. Heitz and J. D. Schall 20130061 20130058 20130067 20130066 20130064 20130056 20130069 20130068 20130071 no. 1629, 5 November 2013 Cellular polarity: from mechanisms to disease Papers of a Discussion Meeting Issue organized and edited by Rafael E. Carazo Salas, Attila Csikász-Nagy and Masamitsu Sato Preface Cell polarity By L. Wolpert 20130419 Introduction Projecting cell polarity into the next decade By A. Csikász-Nagy, M. Sato and R. E. Carazo Salas 20130001 Articles From simple to detailed models for cell polarization By L. Edelstein-Keshet, W. R. Holmes, M. Zajac and M. Dutot Interaction between bud-site selection and polarity-establishment machineries in budding yeast By C.-F. Wu, N. S. Savage and D. J. Lew Actin polymerization or myosin contraction: two ways to build up cortical tension for symmetry breaking By K. Carvalho, J. Lemière, F. Faqir, J. Manzi, L. Blanchoin, J. Plastino, T. Betz and C. Sykes The PAR network: redundancy and robustness in a symmetry-breaking system By F. Motegi and G. Seydoux Functional genomics in the study of yeast cell polarity: moving in the right direction By E. Styles, J.-Y. Youn, M. Mattiazzi Usaj and B. Andrews Epithelial polarity and spindle orientation: intersecting pathways By D. T. Bergstralh, T. Haack and D. St Johnston Spindle orientation and epidermal morphogenesis By A. Kulukian and E. Fuchs Symmetry breaking and polarity establishment during mouse oocyte maturation By K. Yi, B. Rubinstein and R. Li Actin dynamics rapidly reset chemoattractant receptor sensitivity following adaptation in neutrophils By S. N. Dandekar, J. S. Park, G. E. Peng, J. J. Onuffer, W. A. Lim and O. D. Weiner Adaptive molecular networks controlling chemotactic migration: dynamic inputs and selection of the network architecture By H. Chang and A. Levchenko Cell polarity in morphogenesis and metastasis By I. G. Macara and L. McCaffrey Breaking the epithelial polarity barrier in cancer: the strange case of LKB1/PAR-4 By J. I. Partanen, T. A. Tervonen and J. Klefström Phil. Trans. R. Soc. B (2013) 20130003 20130006 20130005 20130010 20130118 20130291 20130016 20130002 20130008 20130117 20130012 20130111 Contents xix Roles of Rho GTPases in leucocyte and leukaemia cell transendothelial migration By E. Infante and A. J. Ridley p120catenin alteration in cancer and its role in tumour invasion By F. Peglion and S. Etienne-Manneville Cell and tissue polarity in the intestinal tract during tumourigenesis: cells still know the right way up, but tissue organization is lost By A. Fatehullah, P. L. Appleton and I. S. Näthke 20130013 20130015 20130014 no. 1630, 19 November 2013 Tool use as adaptation Papers of a Theme Issue compiled and edited by Dora Biro, Michael Haslam and Christian Rutz Introduction Tool use as adaptation By D. Biro, M. Haslam and C. Rutz Articles Tool use by aquatic animals By J. Mann and E. M. Patterson ‘Captivity bias’ in animal tool use and its implications for the evolution of hominin technology By M. Haslam Ecological and social correlates of chimpanzee tool use By C. M. Sanz and D. B. Morgan Risk, mobility or population size? Drivers of technological richness among contact-period western North American hunter—gatherers By M. Collard, B. Buchanan, M. J. O’Brien and J. Scholnick The development of tool manufacture in humans: what helps young children make innovative tools? By J. Chappell, N. Cutting, I. A. Apperly and S. R. Beck The fourth dimension of tool use: temporally enduring artefacts aid primates learning to use tools By D. M. Fragaszy, D. Biro, Y. Eshchar, T. Humle, P. Izar, B. Resende and E. Visalberghi If at first you don’t succeed. . . Studies of ontogeny shed light on the cognitive demands of habitual tool use By E. J. M. Meulman, A. M. Seed and J. Mann Long-tailed macaques select mass of stone tools according to food type By M. D. Gumert and S. Malaivijitnond New Caledonian crows attend to multiple functional properties of complex tools By J. J. H. St Clair and C. Rutz Did tool-use evolve with enhanced physical cognitive abilities? By I. Teschke, C. A. F. Wascher, M. F. Scriba, A. M. P. von Bayern, V. Huml, B. Siemers and S. Tebbich Is primate tool use special? Chimpanzee and New Caledonian crow compared By W. C. McGrew Tool making, hand morphology and fossil hominins By M. W. Marzke Hand before foot? Cortical somatotopy suggests manual dexterity is primitive and evolved independently of bipedalism By T. Hashimoto, K. Ueno, A. Ogawa, T. Asamizuya, C. Suzuki, K. Cheng, M. Tanaka, M. Taoka, Y. Iwamura, G. Suwa and A. Iriki Elongation as a factor in artefacts of humans and other animals: an Acheulean example in comparative context By J. A. J. Gowlett 20120408 20120424 20120421 20120416 20120412 20120409 20120410 20130050 20120413 20120415 20120418 20120422 20120414 20120417 20130114 no. 1631, 5 December 2013 Female competition and aggression Papers of a Theme Issue compiled and edited by Anne Campbell and Paula Stockley Preface The ‘one animal in all creation about which man knows the least’ By S. B. Hrdy Phil. Trans. R. Soc. B (2013) 20130072 xx Contents Introduction Female competition and aggression: interdisciplinary perspectives By P. Stockley and A. Campbell Articles Social competition and selection in males and females By T. H. Clutton-Brock and E. Huchard Intra-sexual selection in cooperative mammals and birds: why are females not bigger and better armed? By A. J. Young and N. C. Bennett Resolving social conflict among females without overt aggression By M. A. Cant and A. J. Young Female competition in chimpanzees By A. E. Pusey and K. Schroepfer-Walker The evolutionary psychology of women’s aggression By A. Campbell The development of human female competition: allies and adversaries By J. F. Benenson Do human females use indirect aggression as an intrasexual competition strategy? By T. Vaillancourt Reproductive competition between females in the matrilineal Mosuo of southwestern China By T. Ji, J.-J. Wu, Q.-Q. He, J.-J. Xu, R. Mace and Y. Tao Wake up and smell the conflict: odour signals in female competition By P. Stockley, L. Bottell and J. L. Hurst Proximate perspectives on the evolution of female aggression: good for the gander, good for the goose? By K. A. Rosvall The influence of androgenic steroid hormones on female aggression in ‘atypical‘ mammals By J. A. French, A. C. Mustoe, J. Cavanaugh and A. K. Birnie Maternal aggression in rodents: brain oxytocin and vasopressin mediate pup defence By O. J. Bosch Corrections Extent and ecological consequences of hunting in Central African rainforests in the twenty-first century By K. A. Abernethy, L. Coad, G. Taylor, M. E. Lee and F. Maisels 20130073 20130074 20130075 20130076 20130077 20130078 20130079 20130080 20130081 20130082 20130083 20130084 20130085 20130494 no. 1632, 19 December 2013 Molecular and functional evolution of transcriptional enhancers in animals Papers of a Theme Issue compiled and edited by Marcelo Rubinstein Introduction Evolution of transcriptional enhancers and animal diversity By M. Rubinstein and F. S. J. de Souza Articles Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution By A. I. Ramos and S. Barolo Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements By H. Guturu, A. C. Doxey, A. M. Wenger and G. Bejerano The mystery of extreme non-coding conservation By N. Harmston, A. Baresić and B. Lenhard Deep conservation of cis-regulatory elements in metazoans By I. Maeso, M. Irimia, J. J. Tena, F. Casares and J. L. Gómez-Skarmeta Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution By N. J. Sakabe and M. A. Nobrega Enhancer turnover and conserved regulatory function in vertebrate evolution By S. Domené, V. F. Bumaschny, F. S. J. de Souza, L. F. Franchini, S. Nasif, M. J. Low and M. Rubinstein Phil. Trans. R. Soc. B (2013) 20130017 20130018 20130029 20130021 20130020 20130022 20130027 Contents xxi Assessing constraints on the path of regulatory sequence evolution By W. J. Glassford and M. Rebeiz The structure and evolution of cis-regulatory regions: the shavenbaby story By D. L. Stern and N. Frankel Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster By A. Glaser-Schmitt, A. Catalán and J. Parsch Many human accelerated regions are developmental enhancers By J. A. Capra, G. D. Erwin, G. McKinsey, J. L. R. Rubenstein and K. S. Pollard A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice By G. B. Kamm, R. López-Leal, J. R. Lorenzo and L. F. Franchini Phil. Trans. R. Soc. B (2013) 20130026 20130028 20130024 20130025 20130019 RSTB_368_1632_Cover_RSTB_368_1632_Cover 30/10/13 6:44 PM Page 2 GUIDANCE FOR AUTHORS Editor Professor Dame Linda Partridge Commissioning Editor Helen Eaton Editorial Board Organismal, environmental and evolutionary biology Professor Spencer Barrett Professor Nick Barton Dr Will Cresswell Professor Sandra Diaz Professor Luc-Alain Giraldeau Professor Patrick Keeling Professor Elena Kramer Professor Georgina Mace Professor Yadvinder Malhi Professor Peter Mumby Professor Karl Sigmund Professor Gabriele Sorci Professor Marcel Visser Professor Andrew Watkinson Cell and developmental biology Dr Buzz Baum Professor Martin Buck Dr Louise Cramer Dr Anne Donaldson Dr Marie-Anne Félix Dr Jeremy Green Professor Laurence Hurst Professor Jack Kaplan Professor Ottoline Leyser Professor Peter Rigby Professor Dale Sanders Dr Krishnaswamy VijayRaghavan Commissioning Editor: Helen Eaton (tel: +44 (0)20 7451 2602 philtransb@royalsociety.org) Editorial Coordinator: Ruth Milne (tel: +44 (0)20 7451 2633; philtransb@royalsociety.org) Production Editor: Tom Lowen 6–9 Carlton House Terrace, London SW1Y 5AG, UK rstb.royalsocietypublishing.org Neuroscience and cognition Dr Brian Billups Professor Colin Blakemore Professor Graham Collingridge Professor Tecumseh Fitch Professor Vittorio Gallese Dr Andrew Glennerster Professor Bill Harris Professor Christian Keysers Professor Hanspeter Mallot Professor Tetsuro Matsuzawa Professor Andrew Whiten Dr Xu Zhang Publishing format Phil. Trans. R. Soc. B articles are published regularly online and in print issues twice a month. Along with all Royal Society journals, we are committed to archiving and providing perpetual access. The journal also offers the facility for including Electronic Supplementary Material (ESM) to papers. Contents of the ESM might include details of methods, derivations of equations, large tables of data, DNA sequences and computer programs. However, the printed version must include enough detail Health and disease Dr Thomas Curran Professor Mark Enright Professor George Gao Professor Christopher Goodnow Dr Julius Hafalla Professor Edward Holmes Professor Dennis Lo Professor Mike Malim Professor Angela McLean Professor Anne O’Garra Dr Mario Recker Professor Nicholas Wald Professor Joanne Webster The Royal Society, the national academy of science of the UK and the Commonwealth, is at the cutting edge of scientific progress. We support many top young scientists, engineers and technologists, influence science policy, debate scientific issues with the public and much more. We are an independent, charitable body and derive our authoritative status from over 1400 Fellows and Foreign Members. AIMS AND SCOPE Each issue of Phil. Trans. R. Soc. B is devoted to a specific area of the biological sciences. This area will define a research frontier that is advancing rapidly, often bridging traditional disciplines. Phil. Trans. R. Soc. B is essential reading for scientists working across the biological sciences. In particular, the journal is focused on the following four cluster areas: neuroscience and cognition; organismal and evolutionary biology; cell and developmental biology; and health and disease. As well as theme issues, the journal publishes papers from the Royal Society’s biological discussion meetings. For information on submitting a proposal for a theme issue, consult the journal‘s website at rstb.royalsocietypublishing.org. Our mission: to expand knowledge and further the role of science and engineering in making the world a better place. The Royal Society’s strategic priorities are to: • invest in future scientific leaders and in • ISBN: 978-1-78252-042-9 Copyright © 2013 The Royal Society Except as otherwise permitted under the Copyright, Designs and Patents Act, 1988, this publication may only be reproduced, stored or transmitted, in any form or by any other means, with the prior permission in writing of the publisher, or in the case of reprographic reproduction, in accordance with the terms of a licence issued by the Copyright Licensing Agency. In particular, the Society permits the making of a single photocopy of an article from this issue (under Sections 29 and 38 of this Act) for an individual for the purposes of research or private study. SUBSCRIPTIONS In 2014 Phil. Trans. R. Soc. B (ISSN 0962-8436) will be published biweekly. Full details of subscriptions and single issue sales may be obtained either by contacting our journal fulfilment agent, Portland Customer Services, Commerce Way, Colchester CO2 8HP; tel: +44 (0)1206 796351; fax: +44 (0)1206 799331; email: sales@portland-services.com or by visiting our website at http://royalsocietypublishing.org/info/subscriptions. The Royal Society is a Registered Charity No. 207043. Selection criteria The criteria for selection are scientific excellence, originality and interest across disciplines within biology. The Editor is responsible for all editorial decisions and she makes these decisions based on the reports received from the referees and/or Editorial Board members. Many more good proposals and articles are submitted to us than we have space to print, we give preference to those that are of broad interest and of high scientific quality. Subscription prices 2014 calendar year UK, Europe and RoW Europe USA, Canada and RoW Electronic access only £2459 €3196 US$4652 Printed version plus electronic access £3442 €4474 US$6512 Typeset in India by Techset Composition Limited, Salisbury, UK. Printed by Latimer Trend, Plymouth. This paper meets the requirements of ISO 9706:1994(E) and ANSI/NISO Z39.48-1992 (Permanence of Paper) effective with volume 335, issue 1273, 1992. Philosophical Transactions of the Royal Society B (ISSN: 0962-8436) is published twice a month for US$6512 per year by the Royal Society, and is distributed in the USA by Agent named Air Business, C/O Worldnet Shipping USA Inc., 149-35 177th Street, Jamaica, New York, NY11434, USA. US Postmaster: Send address changes to Philosophical Transactions of the Royal Society B, C/O Air Business Ltd, C/O Worldnet Shipping USA Inc, 149-35 177th Street Jamaica, New York, NY11414. • • • innovation, influence policymaking with the best scientific advice, invigorate science and mathematics education, increase access to the best science internationally, and inspire an interest in the joy, wonder and excitement of scientific discovery. to satisfy most non-specialist readers. Supplementary data up to 10Mb is placed on the Society's website free of charge. Larger datasets must be deposited in recognised public domain databases by the author. Conditions of publication Articles must not have been published previously, nor be under consideration for publication elsewhere. The main findings of the article should not have been reported in the mass media. Like many journals, Phil. Trans. R. Soc. B employs a strict embargo policy where the reporting of a scientific article by the media is embargoed until a specific time. The Editor has final authority in all matters relating to publication. Electronic Submission details For full submission guidelines and access to all journal content please visit the Phil. Trans. R. Soc. B website at rstb.royalsocietypublishing.org. For further information on the Society’s activities, please contact the following departments on the extensions listed by dialling +44 (0)20 7839 5561, or visit the Society’s Web site (royalsociety.org). Research Support (UK grants and fellowships) Research Appointments (Fellowships): 2542 Research Grants: 2223 International travel Grants: 2555 Newton International Fellowships: 2559 Science Policy Centre General enquiries: 2550 Science Communication General enquiries: 2573 Library and Information Services Library/archive enquiries: 2606 Cover image: Words relating to the title of the Theme Issue are embedded in a background of colour coded DNA sequence logos of hypothetical transcription factor binding sites. Molecular evolution of these sequences may have functional consequences leading to new forms and increasing phenotypic diversity. (Image courtesy of Marcelo Rubinstein.) RSTB_368_1632_Cover_RSTB_368_1632_Cover 30/10/13 6:44 PM Page 1 19 December 2013 volume 368 . number 1632 Molecular and functional evolution of transcriptional enhancers in animals Papers of a Theme Issue compiled and edited by Marcelo Rubinstein Introduction Evolution of transcriptional enhancers and animal diversity M. Rubinstein & F. S. J. de Souza 20130017 Articles Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution A. I. Ramos & S. Barolo 20130018 Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements H. Guturu, A. C. Doxey, A. M. Wenger & G. Bejerano 20130029 20130021 Deep conservation of cis-regulatory elements in metazoans I. Maeso, M. Irimia, J. J. Tena, F. Casares & J. L. Gómez-Skarmeta 20130020 Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution N. J. Sakabe & M. A. Nobrega 20130022 Enhancer turnover and conserved regulatory function in vertebrate evolution S. Domené, V. F. Bumaschny, F. S. J. de Souza, L. F. Franchini, S. Nasif, M. J. Low & M. Rubinstein 20130027 Assessing constraints on the path of regulatory sequence evolution W. J. Glassford & M. Rebeiz 20130026 The structure and evolution of cis-regulatory regions: the shavenbaby story D. L. Stern & N. Frankel 20130028 Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster A. Glaser-Schmitt, A. Catalán & J. Parsch Many human accelerated regions are developmental enhancers J. A. Capra, G. D. Erwin, G. McKinsey, J. L. R. Rubenstein & K. S. Pollard A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice G. B. Kamm, R. López-Leal, J. R. Lorenzo & L. F. Franchini 20130024 20130025 volume 368 number 1632 In this Issue Molecular and functional evolution of transcriptional enhancers in animals Papers of a Theme Issue compiled and edited by Marcelo Rubinstein Enhancer evolution and animal diversity The mystery of extreme non-coding conservation N. Harmston, A. Barešić & B. Lenhard Phil. Trans. R. Soc. B | vol. 368 no. 1632 | 19 December 2013 0962-8436(20131219)368:1632 ISSN 0962-8436 20130019 Volume title page and table of contents Founded in 1660, the Royal Society is the independent scientific academy of the UK, dedicated to promoting excellence in science rstb.royalsocietypublishing.org Published in Great Britain by the Royal Society, 6–9 Carlton House Terrace, London SW1Y 5AG Index Registered Charity No 207043 The world’s first science journal 19 December 2013
