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  • 1.
    Ahlberg, Per E
    et al.
    Natural History Museum of London.
    Luksevics, E.
    Lebedev, O.
    The first tetrapod finds from the Devonian (Upper Famennian) of Latvia1994In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 343, p. 303-328Article in journal (Refereed)
  • 2.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sensory exploitation and sexual conflict2006In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 361, no 1466, p. 375-386Article in journal (Refereed)
  • 3.
    Beekman, Madeleine
    et al.
    Univ Sydney, Sch Life & Environm Sci, Sydney, NSW 2006, Australia..
    Nieuwenhuis, Bart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ortiz-Barrientos, Daniel
    Univ Queensland, Sch Biol Sci, St Lucia, Qld, Australia..
    Evans, Jonathan P.
    Univ Western Australia, Sch Anim Biol, Ctr Evolutionary Biol, Nedlands, WA 6009, Australia..
    Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi2016In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, no 1706, article id 20150541Article, review/survey (Refereed)
    Abstract [en]

    Darwin was the first to recognize that sexual selection is a strong evolutionary force. Exaggerated traits allow same-sex individuals to compete over access to mates and provide a mechanism by which mates are selected. It is relatively easy to appreciate how inter-and intrasexual selection work in organisms with the sensory capabilities to perceive physical or behavioural traits that signal mate quality or mate compatibility, and to assess the relative quality of competitors. It is therefore not surprising that most studies of sexual selection have focused on animals with separate sexes and obvious adaptations that function in the context of reproductive competition. Yet, many sexual organisms are both male and female at the same time, often lack sexual dimorphism and never come into direct contact at mating. How does sexual selection act in such species, and what can we learn from them? Here, we address these questions by exploring the potential for sexual selection in simultaneous hermaphrodites, sperm-and broadcast spawners, plants and fungi. Our reviewreveals a range of mechanisms of sexual selection, operating primarily after gametes have been released, which are common in many of these groups and also quite possibly in more familiar (internally fertilizing and sexually dimorphic) organisms. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  • 4.
    Bentley, Katie
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology. Harvard Med Sch, Beth Israel Deaconess Med Ctr, Computat Biol Lab, Boston, MA USA..
    Chakravartula, Shilpa
    Harvard Med Sch, Beth Israel Deaconess Med Ctr, Computat Biol Lab, Boston, MA USA..
    The temporal basis of angiogenesis2017In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1720, p. 1-11, article id 20150522Article in journal (Refereed)
    Abstract [en]

    The process of new blood vessel growth (angiogenesis) is highly dynamic, involving complex coordination of multiple cell types. Though the process must carefully unfold over time to generate functional, well-adapted branching networks, we seldom hear about the time-based properties of angiogenesis, despite timing being central to other areas of biology. Here, we present a novel, time-based formulation of endothelial cell behaviour during angiogenesis and discuss a flurry of our recent, integrated in silico/in vivo studies, put in context to the wider literature, which demonstrate that tissue conditions can locally adapt the timing of collective cell behaviours/decisions to grow different vascular network architectures. A growing array of seemingly unrelated 'temporal regulators' have recently been uncovered, including tissue derived factors (e.g. semaphorins or the high levels of VEGF found in cancer) and cellular processes (e.g. asymmetric cell division or filopodia extension) that act to alter the speed of cellular decisions to migrate. We will argue that 'temporal adaptation' provides a novel account of organ/disease-specific vascular morphology and reveals 'timing' as a new target for therapeutics. We therefore propose and explain a conceptual shift towards a 'temporal adaptation' perspective in vascular biology, and indeed other areas of biology where timing remains elusive. This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.

  • 5.
    Budd, Graham
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Early animal evolution and the origins of nervous systems2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1684, article id 20150037Article in journal (Refereed)
    Abstract [en]

    Understanding the evolution of early nervous systems is hazardous because we lack good criteria for determining homology between the systems of distant taxa; the timing of the evolutionary events is contested, and thus the relevant ecological and geological settings for them are also unclear. Here I argue that no simple approach will resolve the first issue, but that it remains likely that animals evolved relatively late, and that their nervous systems thus arose during the late Ediacaran, in a context provided by the changing planktonic and benthic environments of the time. The early trace fossil provides the most concrete evidence for early behavioural diversification, but it cannot simply be translated into increasing nervous system complexity: behavioural complexity does not map on a one-to-one basis onto nervous system complexity, both because of possible limitations to behaviour caused by the environment and because we know that even organisms without nervous systems are capable of relatively complex behaviour.

  • 6.
    Budd, Graham E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    The earliest fossil record of the animals and its significance2008In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 363, no 1496, p. 1425-1434Article, review/survey (Refereed)
    Abstract [en]

    The fossil record of the earliest animals has been enlivened in recent years by a series of spectacular discoveries, including embryos, from the Ediacaran to the Cambrian, but many issues, not least of dating and interpretation, remain controversial. In particular, aspects of taphonomy of the earliest fossils require careful consideration before pronouncements about their affinities. Nevertheless, a reasonable case can now be made for the extension of the fossil record of at least basal animals (sponges and perhaps cnidarians) to a period of time significantly before the beginning of the Cambrian. The Cambrian explosion itself still seems to represent the arrival of the bilaterians, and many new fossils in recent years have added significant data on the origin of the three major bilaterian clades. Why animals appear so late in the fossil record is still unclear, but the recent trend to embrace rising oxygen levels as being the proximate cause remains unproven and may even involve a degree of circularity.

  • 7.
    Budd, Graham
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Jackson, Illiam
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Ecological innovations in the Cambrian and the origins of the crown group phyla2016In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, no 1685Article in journal (Refereed)
    Abstract [en]

    Simulation studies of the early origins of the modern phyla in the fossil record, and the rapid diversification that led to them, show that these are inevitable outcomes of rapid and long-lasting radiations. Recent advances in Cambrian stratigraphy have revealed a more precise picture of the early bilaterian radiation taking place during the earliest Terreneuvian Series, although several ambiguities remain. The early period is dominated by various tubes and a moderately diverse trace fossil record, with the classical ‘Tommotian’ small shelly biota beginning to appear some millions of years after the base of the Cambrian at ca 541 Ma. The body fossil record of the earliest period contains a few representatives of known groups, but most of the record is of uncertain affinity. Early trace fossils can be assigned to ecdysozoans, but deuterostome and even spiralian trace and body fossils are less clearly represented. One way of explaining the relative lack of clear spiralian fossils until about 536 Ma is to assign the various lowest Cambrian tubes to various stem-group lophotrochozoans, with the implication that the groundplan of the lophotrochozoans included a U-shaped gut and a sessile habit. The implication of this view would be that the vagrant lifestyle of annelids, nemerteans and molluscs would be independently derived from such a sessile ancestor, with potentially important implications for the homology of their sensory and nervous systems.

  • 8. Chapman, Henry N.
    et al.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Diffraction before destruction2014In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1647, p. 20130313-Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.

  • 9.
    Colautti, Robert I.
    et al.
    Queens Univ, Dept Biol, 116 Barrie St, Kingston, ON K7L 3N6, Canada..
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Jill T.
    Univ Georgia, Dept Genet, 120 Green St, Athens, GA 30602 USA.;Univ Georgia, Odum Sch Ecol, 120 Green St, Athens, GA 30602 USA..
    Phenological shifts of native and invasive species under climate change: insights from the Boechera - Lythrum model2017In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1712, article id 20160032Article, review/survey (Refereed)
    Abstract [en]

    Warmer and drier climates have shifted phenologies of many species. However, the magnitude and direction of phenological shifts vary widely among taxa, and it is often unclear when shifts are adaptive or how they affect long-term viability. Here, we model evolution of flowering phenology based on our long-term research of two species exhibiting opposite shifts in floral phenology: Lythrum salicaria, which is invasive in North America, and the sparse Rocky Mountain native Boechera stricta. Genetic constraints are similar in both species, but differences in the timing of environmental conditions that favour growth lead to opposite phenological shifts under climate change. As temperatures increase, selection is predicted to favour earlier flowering in native B. stricta while reducing population viability, even if populations adapt rapidly to changing environmental conditions. By contrast, warming is predicted to favour delayed flowering in both native and introduced L. salicaria populations while increasing long-term viability. Relaxed selection from natural enemies in invasive L. salicaria is predicted to have little effect on flowering time but a large effect on reproductive fitness. Our approach highlights the importance of understanding ecological and genetic constraints to predict the ecological consequences of evolutionary responses to climate change on contemporary timescales. This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

  • 10. Doolittle, W F
    et al.
    Boucher, Y
    Nesbø, C L
    Douady, C J
    Andersson, Jan O
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 1X5, Canada .
    Roger, A J
    How big is the iceberg of which organellar genes in nuclear genomes are but the tip?2003In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 358, no 1429, p. 39-58; discussion 57Article in journal (Refereed)
    Abstract [en]

    As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.

  • 11. Gerbault, Pascale
    et al.
    Liebert, Anke
    Itan, Yuval
    Powell, Adam
    Currat, Mathias
    Burger, Joachim
    Swallow, Dallas M.
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolution of lactase persistence: an example of human niche construction2011In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 366, no 1566, p. 863-877Article in journal (Refereed)
    Abstract [en]

    Niche construction is the process by which organisms construct important components of their local environment in ways that introduce novel selection pressures. Lactase persistence is one of the clearest examples of niche construction in humans. Lactase is the enzyme responsible for the digestion of the milk sugar lactose and its production decreases after the weaning phase in most mammals, including most humans. Some humans, however, continue to produce lactase throughout adulthood, a trait known as lactase persistence. In European populations, a single mutation (-13910*T) explains the distribution of the phenotype, whereas several mutations are associated with it in Africa and the Middle East. Current estimates for the age of lactase persistence-associated alleles bracket those for the origins of animal domestication and the culturally transmitted practice of dairying. We report new data on the distribution of -13910*T and summarize genetic studies on the diversity of lactase persistence worldwide. We review relevant archaeological data and describe three simulation studies that have shed light on the evolution of this trait in Europe. These studies illustrate how genetic and archaeological information can be integrated to bring new insights to the origins and spread of lactase persistence. Finally, we discuss possible improvements to these models.

  • 12.
    Grace, Delia
    et al.
    Int Livestock Res Inst, Box 30709, Nairobi, Kenya..
    Lindahl, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Int Livestock Res Inst, Box 30709, Nairobi, Kenya..
    Wanyoike, Francis
    Int Livestock Res Inst, Box 30709, Nairobi, Kenya..
    Bett, Bernard
    Int Livestock Res Inst, Box 30709, Nairobi, Kenya..
    Randolph, Tom
    Int Livestock Res Inst, Box 30709, Nairobi, Kenya..
    Rich, Karl M.
    Lincoln Univ, Lincoln 7647, New Zealand..
    Poor livestock keepers: ecosystem – poverty – health interactions2017In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1725, article id 20160166Article in journal (Refereed)
    Abstract [en]

    Humans have never been healthier, wealthier or more numerous. Yet, present success may be at the cost of future prosperity and in some places, especially in sub-Saharan Africa, poverty persists. Livestock keepers, especially pastoralists, are over-represented among the poor. Poverty has been mainly attributed to a lack of access, whether to goods, education or enabling institutions. More recent insights suggest ecosystems may influence poverty and the self-reinforcing mechanisms that constitute poverty traps in more subtle ways. The plausibility of zoonoses as poverty traps is strengthened by landmark studies on disease burden in recent years. While in theory, endemic zoonoses are best controlled in the animal host, in practice, communities are often left to manage disease themselves, with the focus on treatment rather than prevention. We illustrate this with results from a survey on health costs in a pastoral ecosystem. Epidemic zoonoses are more likely to elicit official responses, but these can have unintended consequences that deepen poverty traps. In this context, a systems understanding of disease control can lead to more effective and pro-poor disease management. We illustrate this with an example of how a system dynamics model can help optimize responses to Rift Valley fever outbreaks in Kenya by giving decision makers real-time access to the costs of the delay in vaccinating. In conclusion, a broader, more ecological understanding of poverty and of the appropriate responses to the diseases of poverty can contribute to improved livelihoods for livestock keepers in Africa.

    This article is part of the themed issue 'One Health for a changing world: zoonoses, ecosystems and human well-being'.

  • 13.
    Hammarström, Leif
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Styring, Stenbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Coupled electron transfers in artificial photosynthesis2008In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 363, no 1494, p. 1283-1291Article in journal (Refereed)
    Abstract [en]

    Light-induced charge separation in molecular assemblies has been widely investigated in the context of artificial photosynthesis. Important progress has been made in the fundamental understanding of electron and energy transfer and in stabilizing charge separation by multi-step electron transfer. In the Swedish Consortium for Artificial Photosynthesis, we build on principles from the natural enzyme photosystem II and Fe-hydrogenases. An important theme in this biomimetic effort is that of coupled electron-transfer reactions, which have so far received only little attention. (i) Each absorbed photon leads to charge separation on a single-electron level only, while catalytic water splitting and hydrogen production are multi-electron processes; thus there is the need for controlling accumulative electron transfer on molecular components. (ii) Water splitting and proton reduction at the potential catalysts necessarily require the management of proton release and/or uptake. Far from being just a stoichiometric requirement, this controls the electron transfer processes by proton-coupled electron transfer (PCET). (iii) Redox-active links between the photosensitizers and the catalysts are required to rectify the accumulative electron-transfer reactions, and will often be the starting points of PCET.

  • 14.
    Hjort, Karin
    et al.
    Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK.
    Goldberg, Alina V
    Tsaousis, Anastasios D
    Hirt, Robert P
    Embley, T Martin
    Diversity and reductive evolution of mitochondria among microbial eukaryotes2010In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 365, no 1541, p. 713-27Article in journal (Refereed)
    Abstract [en]

    All extant eukaryotes are now considered to possess mitochondria in one form or another. Many parasites or anaerobic protists have highly reduced versions of mitochondria, which have generally lost their genome and the capacity to generate ATP through oxidative phosphorylation. These organelles have been called hydrogenosomes, when they make hydrogen, or remnant mitochondria or mitosomes when their functions were cryptic. More recently, organelles with features blurring the distinction between mitochondria, hydrogenosomes and mitosomes have been identified. These organelles have retained a mitochondrial genome and include the mitochondrial-like organelle of Blastocystis and the hydrogenosome of the anaerobic ciliate Nyctotherus. Studying eukaryotic diversity from the perspective of their mitochondrial variants has yielded important insights into eukaryote molecular cell biology and evolution. These investigations are contributing to understanding the essential functions of mitochondria, defined in the broadest sense, and the limits to which reductive evolution can proceed while maintaining a viable organelle.

  • 15.
    Kazancioglu, Erem
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Alonzo, Suzanne H.
    The evolution of optimal female mating rate changes the coevolutionary dynamics of female resistance and male persistence2012In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 367, no 1600, p. 2339-2347Article in journal (Refereed)
    Abstract [en]

    Mating decisions usually involve conflict of interests between sexes. Accordingly, males benefit from increased number of matings, whereas costs of mating favour a lower mating rate for females. The resulting sexual conflict underlies the coevolution of male traits that affect male mating success ('persistence') and female traits that affect female mating patterns ('resistance'). Theoretical studies on the coevolutionary dynamics of male persistence and female resistance assumed that costs of mating and, consequently, the optimal female mating rate are evolutionarily constant. Costs of mating, however, are often caused by male 'persistence' traits that determine mating success. Here, we present a model where the magnitude of costs of mating depend on, and evolve with, male persistence. We find that allowing costs of mating to depend on male persistence results in qualitatively different coevolutionary dynamics. Specifically, we find that male traits such as penis spikes that harm females are not predicted to exhibit runaway selection with female resistance, in contrast to previous theory that predicts indefinite escalation. We argue that it is essential to determine when and to what extent costs of mating are caused by male persistence in order to understand and accurately predict coevolutionary dynamics of traits involved in mating decisions.

  • 16.
    Krause, J.
    et al.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Biol & Ecol Fishes, Muggelseedamm 310, D-12587 Berlin, Germany.;Humboldt Univ, Fac Life Sci, Albrecht Daniel Thaer Inst, Invalidenstr 42, D-10115 Berlin, Germany..
    Herbert-Read, James E.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics. Stockholm Univ, Dept Zool, Stockholm, Sweden..
    Seebacher, F.
    Univ Sydney, Sch Life & Environm Sci, Sydney, NSW 2006, Australia..
    Domenici, P.
    CNR, IAMC CNR, Ist Ambiente Marino Costiero, I-09170 Torregrande, Oristano, Italy..
    Wilson, A. D. M.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Biol & Ecol Fishes, Muggelseedamm 310, D-12587 Berlin, Germany.;Stockholm Univ, Dept Zool, Stockholm, Sweden..
    Marras, S.
    CNR, IAMC CNR, Ist Ambiente Marino Costiero, I-09170 Torregrande, Oristano, Italy..
    Svendsen, M. B. S.
    Univ Copenhagen, Marine Biol Sect, Strandpromenaden 5, DK-3000 Helsingor, Denmark..
    Strömbom, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics. Lafayette Coll, Dept Biol, Easton, PA 18042 USA..
    Steffensen, J. F.
    Univ Copenhagen, Marine Biol Sect, Strandpromenaden 5, DK-3000 Helsingor, Denmark..
    Krause, S.
    Lubeck Univ Appl Sci, Dept Elect Engn & Comp Sci, D-23562 Lubeck, Germany..
    Viblanc, P. E.
    Humboldt Univ, Fac Life Sci, Albrecht Daniel Thaer Inst, Invalidenstr 42, D-10115 Berlin, Germany..
    Couillaud, P.
    Univ Paris 06, Dept Licence Sci & Technol, 4 Pl Jussieu, F-75005 Paris, France..
    Bach, P.
    Inst Rech Dev, UMR MARBEC 248, 0b7,Ave Jean Monnet,CS 30171,, F-34203 Sete, France..
    Sabarros, P. S.
    Inst Rech Dev, UMR MARBEC 248, 0b7,Ave Jean Monnet,CS 30171,, F-34203 Sete, France..
    Zaslansky, P.
    Charite, Julius Wolff Inst Biomechan & Musculoskeletal Reg, Philippstr 13,Haus 11, D-10115 Berlin, Germany..
    Kurvers, R. H. J. M.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Biol & Ecol Fishes, Muggelseedamm 310, D-12587 Berlin, Germany.;Max Planck Inst Human Dev, Ctr Adapt Rat, Lentzeallee 94, D-14195 Berlin, Germany..
    Injury-mediated decrease in locomotor performance increases predation risk in schooling fish2017In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1727, article id 20160232Article in journal (Refereed)
    Abstract [en]

    The costs and benefits of group living often depend on the spatial position of individuals within groups and the ability of individuals to occupy preferred positions. For example, models of predation events for moving prey groups predict higher mortality risk for individuals at the periphery and front of groups. We investigated these predictions in sardine (Sardinella aurita) schools under attack from group hunting sailfish (Istiophorus platypterus) in the open ocean. Sailfish approached sardine schools about equally often from the front and rear, but prior to attack there was a chasing period in which sardines attempted to swim away from the predator. Consequently, all sailfish attacks were directed at the rear and peripheral positions of the school, resulting in higher predation risk for individuals at these positions. During attacks, sailfish slash at sardines with their bill causing prey injury including scale removal and tissue damage. Sardines injured in previous attacks were more often found in the rear half of the school than in the front half. Moreover, injured fish had lower tail-beat frequencies and lagged behind uninjured fish. Injuries inflicted by sailfish bills may, therefore, hinder prey swimming speed and drive spatial sorting in prey schools through passive self-assortment. We found only partial support for the theoretical predictions from current predator-prey models, highlighting the importance of incorporating more realistic predator-prey dynamics into these models. This article is part of the themed issue 'Physiological determinants of social behaviour in animals'.

  • 17. Krzewinska, Maja
    et al.
    Bjornstad, Gro
    Skoglund, Pontus
    Ólason, Páll Isolfur
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Bill, Jan
    Gotherstrom, Anders
    Hagelberg, Erika
    Mitochondrial DNA variation in the Viking age population of Norway2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1660, p. 20130384-Article in journal (Refereed)
    Abstract [en]

    The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.

  • 18.
    Larhammar, Dan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Pharmacology.
    Nordström, Karin
    School of Molecular and Biomedical Science, The University of Adelaide, Adelaide SA 5005, Australia .
    Larsson, Tomas A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Pharmacology.
    Evolution of vertebrate rod and cone phototransduction genes2009In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 364, no 1531, p. 2867-2880Article, review/survey (Refereed)
    Abstract [en]

    Vertebrate cones and rods in several cases use separate but related components for their signal transduction (opsins, G-proteins, ion channels, etc.). Some of these proteins are also used differentially in other cell types in the retina. Because cones, rods and other retinal cell types originated in early vertebrate evolution, it is of interest to see if their specific genes arose in the extensive gene duplications that took place in the ancestor of the jawed vertebrates (gnathostomes) by two tetraploidizations (genome doublings). The ancestor of teleost fishes subsequently underwent a third tetraploidization. Our previously reported analyses showed that several gene families in the vertebrate visual phototransduction cascade received new members in the basal tetraploidizations. We here expand these data with studies of additional gene families and vertebrate species. We conclude that no less than 10 of the 13 studied phototransduction gene families received additional members in the two basal vertebrate tetraploidizations. Also the remaining three families seem to have undergone duplications during the same time period but it is unclear if this happened as a result of the tetraploidizations. The implications of the many early vertebrate gene duplications for functional specialization of specific retinal cell types, particularly cones and rods, are discussed.

  • 19.
    Malmström, Helena Jankovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Linderholm, Anna
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Stora, Jan
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gilbert, M. Thomas P.
    Holmlund, Gunilla
    Willerslev, Eske
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Liden, Kerstin
    Gotherstrom, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1660, p. 20130373-Article in journal (Refereed)
    Abstract [en]

    The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.

  • 20. Nebert, Daniel W.
    et al.
    Wikvall, Kjell
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Miller, Walter L.
    Human cytochromes P450 in health and disease2013In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 368, no 1612, p. 20120431-Article, review/survey (Refereed)
    Abstract [en]

    There are 18 mammalian cytochrome P450 (CYP) families, which encode 57 genes in the human genome. CYP2, CYP3 and CYP4 families contain far more genes than the other 15 families; these three families are also the ones that are dramatically larger in rodent genomes. Most (if not all) genes in the CYP1, CYP2, CYP3 and CYP4 families encode enzymes involved in eicosanoid metabolism and are inducible by various environmental stimuli (i.e. diet, chemical inducers, drugs, pheromones, etc.), whereas the other 14 gene families often have only a single member, and are rarely if ever inducible or redundant. Although the CYP2 and CYP3 families can be regarded as largely redundant and promiscuous, mutations or other defects in one or more genes of the remaining 16 gene families are primarily the ones responsible for P450-specific diseases-confirming these genes are not superfluous or promiscuous but rather are more directly involved in critical life functions. P450-mediated diseases comprise those caused by: aberrant steroidogenesis; defects in fatty acid, cholesterol and bile acid pathways; vitamin D dysregulation and retinoid (as well as putative eicosanoid) dysregulation during fertilization, implantation, embryogenesis, foetogenesis and neonatal development.

  • 21.
    Nieuwenhuis, Bart P. S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, 830 North Univ, Ann Arbor, MI 48109 USA..
    The frequency of sex in fungi2016In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, no 1706, article id 20150540Article, review/survey (Refereed)
    Abstract [en]

    Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  • 22.
    Parducci, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Väliranta, Minna
    Salonen, J. Sakari
    Ronkainen, Tiina
    Matetovici, Irina
    Fontana, Sonia L.
    Eskola, Tiina
    Sarala, Pertti
    Suyama, Yoshihisa
    Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1660, p. 20130382-Article in journal (Refereed)
    Abstract [en]

    We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.

  • 23.
    Pavlov, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Liljas, Anders
    Dept Biochem & Struct Biol, Lund University..
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    A recent intermezzo at the Ribosome Club2017In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1716, article id 20160185Article, review/survey (Refereed)
    Abstract [en]

    Two sets of ribosome structures have recently led to two different interpretations of what limits the accuracy of codon translation by transfer RNAs. In this review, inspired by this intermezzo at the Ribosome Club, we briefly discuss accuracy amplification by energy driven proofreading and its implementation in genetic code translation. We further discuss general ways by which the monitoring bases of 16S rRNA may enhance the ultimate accuracy (d-values) and how the codon translation accuracy is reduced by the actions of Mg2+ ions and the presence of error inducing aminoglycoside antibiotics. We demonstrate that complete freezing-in of cognate-like tautomeric states of ribosome-bound nucleotide bases in transfer RNA or messenger RNA is not compatible with recent experiments on initial codon selection by transfer RNA in ternary complex with elongation factor Tu and GTP. From these considerations, we suggest that the sets of 30S subunit structures from the Ramakrishnan group and 70S structures from the Yusupov/Yusupova group may, after all, reflect two sides of the same coin and how the structurally based intermezzo at the Ribosome Club may be resolved simply by taking the dynamic aspects of ribosome function into account. This article is part of the themed issue 'Perspectives on the ribosome'.

  • 24.
    Qvarnström, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Rice, Amber M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Speciation in Ficedula flycatchers2010In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 365, no 1547, p. 1841-1852Article, review/survey (Refereed)
    Abstract [en]

    Speciation in animals often requires that population divergence goes through three major evolutionary stages, i.e. ecological divergence, development of sexual isolation and the build-up of genetic incompatibility. There is theoretical consensus regarding favourable conditions required for speciation to reach its final and irreversible stage, but empirical tests remain rare. Here, we review recent research on processes of speciation, based on studies in hybrid zones between collared (Ficedula albicollis) and pied flycatchers (Ficedula hypoleuca). A major advantage of this study system is that questions concerning all three major sources of reproductive isolation and their interconnections can be addressed. We conclude that (i) ecological divergence is caused by divergence in life-history traits, (ii) females prefer mates of their own species based on differences in both plumage and song characteristics, (iii) male plumage characteristics have diverged but their song has converged in sympatry, (iv) there is genetic incompatibility in accordance with Haldane's rule, and (v) the Z-chromosome appears to be a hotspot for genes involved in sexual isolation and genetic incompatibility. We discuss how identification of the genes underlying the three major sources of reproductive isolation can be used to draw conclusions about links between the processes driving their evolution.

  • 25.
    Ratnakumar, Abhirami
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mousset, Sylvain
    Glémin, Sylvain
    Berglund, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Galtier, Nicolas
    Duret, Laurent
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Detecting positive selection within genomes: the problem of biased gene conversion2010In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 365, no 1552, p. 2571-2580Article in journal (Refereed)
    Abstract [en]

    The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio (d(N)/d(S)), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d(N)/d(S) (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.

  • 26.
    Saw, Jimmy H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Juzokaite, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden..
    Dodsworth, Jeremy A.
    Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA..
    Murugapiran, Senthil K.
    Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA..
    Colman, Dan R.
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA..
    Takacs-Vesbach, Cristina
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA..
    Hedlund, Brian P.
    Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA..
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1678, article id 20140328Article in journal (Refereed)
    Abstract [en]

    The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteo-bacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.

  • 27.
    Sumpter, David J. T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Pratt, Stephen C.
    Quorum responses and consensus decision making2009In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 364, no 1518, p. 743-753Article in journal (Refereed)
    Abstract [en]

    Animal groups are said to make consensus decisions when groupmembers come to agree on the same option. Consensus decisions are taxonomically widespread and potentially offer three key benefits: maintenance of group cohesion, enhancement of decision accuracy compared with lone individuals and improvement in decision speed. In the absence of centralized control, arriving at a consensus depends on local interactions in which each individual's likelihood of choosing an option increases with the number of others already committed to that option. The resulting positive feedback can effectively direct most or all group members to the best available choice. In this paper, we examine the functional form of the individual response to others' behaviour that lies at the heart of this process. We review recent theoretical and empirical work on consensus decisions, and we develop a simple mathematical model to show the central importance to speedy and accurate decisions of quorum responses, in which an animal's probability of exhibiting a behaviour is a sharply nonlinear function of the number of other individuals already performing this behaviour. We argue that systems relying on such quorum rules can achieve cohesive choice of the best option while also permitting adaptive tuning of the trade-off between decision speed and accuracy.

  • 28.
    Säfholm, Moa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Ribbenstedt, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Fick, Jerker
    Berg, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Risks of hormonally active pharmaceuticals to amphibians: a growing concern regarding progestagens2014In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1656, p. 20130577-Article in journal (Refereed)
    Abstract [en]

    Most amphibians breed in water, including the terrestrial species, and may therefore be exposed to water-borne pharmaceuticals during critical phases of the reproductive cycle, i.e. sex differentiation and gamete maturation. The objectives of this paper were to (i) review available literature regarding adverse effects of hormonally active pharmaceuticals on amphibians, with special reference to environmentally relevant exposure levels and (ii) expand the knowledge on toxicity of progestagens in amphibians by determining effects of norethindrone (NET) and progesterone (P) exposure to 0, 1, 10 or 100 ng l(-1) (nominal) on oogenesis in the test species Xenopus tropicalis. Very little information was found on toxicity of environmentally relevant concentrations of pharmaceuticals on amphibians. Research has shown that environmental concentrations (1.8 ng l(-1)) of the pharmaceutical oestrogen ethinylestradiol (EE2) cause developmental reproductive toxicity involving impaired spermatogenesis in frogs. Recently, it was found that the progestagen levonorgestrel (LNG) inhibited oogenesis in frogs by interrupting the formation of vitellogenic oocytes at an environmentally relevant concentration (1.3 ng l(-1)). Results from the present study revealed that 1 ng NET l(-1) and 10 ng P l(-1) caused reduced proportions of vitellogenic oocytes and increased proportions of previtellogenic oocytes compared with the controls, thereby indicating inhibited vitellogenesis. Hence, the available literature shows that the oestrogen EE2 and the progestagens LNG, NET and P impair reproductive functions in amphibians at environmentally relevant exposure concentrations. The progestagens are of particular concern given their prevalence, the range of compounds and that several of them (LNG, NET and P) share the same target (oogenesis) at environmental exposure concentrations, indicating a risk for adverse effects on fertility in exposed wild amphibians.

  • 29.
    Tullberg, Birgitta S.
    et al.
    Zoologiska institutionen, Stockholms universitet.
    Ah-King, Malin
    Zoologiska institutionen, Stockholms universitet.
    Temrin, Hans
    Zoologiska institutionen, Stockholms universitet.
    Phylogenetic reconstruction of the parental-care system in the ancestors of birds2002In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 357, p. 251-257Article in journal (Refereed)
    Abstract [en]

    Due to the controversy surrounding incipient avian parental care, ancestral parental care systems werereconstructed in a phylogeny including major extant amniote lineages. Using two different resolutions forthe basal avian branches, transitions between the states no care, female care, biparental care and malecare were inferred for the most basal branches of the tree. Uniparental female care was inferred for thelineage to birds and crocodiles. Using a phylogeny where ratites and tinamous branch off early and anordered character-state assumption, a transition to biparental care was inferred for the ancestor of birds.This ancestor could be any organism along the lineage leading from the crocodile–bird split up to modernbirds, not necessarily the original bird. We discuss the support for alternative avian phylogenies and thehomology in parental care between crocodiles and birds. We suggest that the phylogenetic pattern shouldbe used as a starting point for a more detailed analysis of parental care systems in birds and their relatives.

  • 30.
    Ullman, Gustaf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Walldén, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mahmutovic, Anel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Razinkov, Ivan
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking2013In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 368, no 1611, p. 20120025:1-8Article in journal (Refereed)
  • 31.
    Vreeburg, Sabine
    et al.
    Wageningen Univ, Plant Sci Grp, Genet Lab, NL-6700 AA Wageningen, Netherlands..
    Nygren, Kristiina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Wageningen Univ, Plant Sci Grp, Genet Lab, NL-6700 AA Wageningen, Netherlands..
    Aanen, Duur K.
    Wageningen Univ, Plant Sci Grp, Genet Lab, NL-6700 AA Wageningen, Netherlands..
    Unholy marriages and eternal triangles: how competition in the mushroom life cycle can lead to genomic conflict2016In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, no 1706, article id 20150533Article, review/survey (Refereed)
    Abstract [en]

    In the vast majority of sexual life cycles, fusion between single-celled gametes is directly followed by nuclear fusion, leading to a diploid zygote and a lifelong commitment between two haploid genomes. Mushroom-forming basidiomycetes differ in two key respects. First, the multicellular haploid mating partners are fertilized in their entirety, each cell being a gamete that simultaneously can behave as a female, i.e. contributing the cytoplasm to a zygote by accepting nuclei, and a male gamete, i.e. only donating nuclei to the zygote. Second, after gamete union, the two haploid genomes remain separate so that the main vegetative stage, the dikaryon, has two haploid nuclei per cell. Only when the dikaryon produces mushrooms, do the nuclei fuse to enter a short diploid stage, immediately followed by meiosis and haploid spore formation. So in basidiomycetes, gamete fusion and genome mixing (sex) are separated in time. The 'living apart together' of nuclei in the dikaryon maintains some autonomy for nuclei to engage in a relationship with a different nucleus. We show that competition among the two nuclei of the dikaryon for such 'extramarital affairs' may lead to genomic conflict by favouring genes beneficial at the level of the nucleus, but deleterious at that of the dikaryon. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  • 32.
    Westermark, Per
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Westermark, Gunilla T
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Reflections on amyloidosis in Papua New Guinea2008In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 363, no 1510, p. 3701-3705Article, review/survey (Refereed)
    Abstract [en]

    The amyloidoses comprise a heterogeneous group of diseases in which 1 out of more than 25 human proteins aggregates into characteristic beta-sheet fibrils with some unique properties. Aggregation is nucleation dependent. Among the known amyloid-forming constituents is the prion protein, well known for its ability to transmit misfolding and disease from one individual to another. There is increasing evidence that other amyloid forms also may be transmissible but only if certain prerequisites are fulfilled. One of these forms is systemic AA-amyloidosis in which an acute-phase reactant, serum AA, is over-expressed and, possibly after cleavage, aggregates into amyloid fibrils, causing disease. In a mouse model, this disorder can easily be transmitted from one animal to another both by intravenous and oral routes. Also, synthetic amyloid-like fibrils made from defined small peptides have this property, indicating a prion-like transmission mechanism. Even some fibrils occurring in the environment can transmit AA-amyloidosis in the murine model. AA-amyloidosis is particularly common in certain areas of Papua New Guinea, probably due to the endemicity of malaria and perhaps genetic predisposition. Now, when kuru is disappearing, more interest should be focused on the potentially lethal systemic AA-amyloidosis.

  • 33.
    Williams, A
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Carlson, SJ
    Brunton, CHC
    Holmer, L. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Popov, L
    A supra-ordinal classification of the Brachiopoda1996In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 351, no 1344, p. 1171-1193Article in journal (Refereed)
    Abstract [en]

    A new classification of the Brachiopoda is proposed to take into account recent advances in our understanding of the anatomy, shell morphology, ontogeny and phylogeny of the phylum. The use of phylogenetic analysis to help rationalize this new information

  • 34. Willis, K. J.
    et al.
    Bennett, Keith D.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Burrough, S. L.
    Macias-Fauria, M.
    Tovar, C.
    Determining the response of African biota to climate change: using the past to model the future2013In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 368, no 1625, p. 20120491-Article, review/survey (Refereed)
    Abstract [en]

    Prediction of biotic responses to future climate change in tropical Africa tends to be based on two modelling approaches: bioclimatic species envelope models and dynamic vegetation models. Another complementary but underused approach is to examine biotic responses to similar climatic changes in the past as evidenced in fossil and historical records. This paper reviews these records and highlights the information that they provide in terms of understanding the local-and regional-scale responses of African vegetation to future climate change. A key point that emerges is that a move to warmer and wetter conditions in the past resulted in a large increase in biomass and a range distribution of woody plants up to 400-500 km north of its present location, the so-called greening of the Sahara. By contrast, a transition to warmer and drier conditions resulted in a reduction in woody vegetation in many regions and an increase in grass/savanna-dominated landscapes. The rapid rate of climate warming coming into the current interglacial resulted in a dramatic increase in community turnover, but there is little evidence for widespread extinctions. However, huge variation in biotic response in both space and time is apparent with, in some cases, totally different responses to the same climatic driver. This highlights the importance of local features such as soils, topography and also internal biotic factors in determining responses and resilience of the African biota to climate change, information that is difficult to obtain from modelling but is abundant in palaeoecological records.

  • 35. Willis, Katherine J.
    et al.
    Miguel B. Araújo, Miguel B.
    Bennett, Keith
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Blanca Figueroa-Rangel, Blanca
    Froyd, Cynthia A.
    Myers, Norman
    How can a knowledge of the past help to conserve the future? Biodiversity conservation and the relevance of long-term ecological studies2007In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 362, no 1478, p. 175-186Article in journal (Refereed)
    Abstract [en]

    This paper evaluates how long-term records could and should be utilized in conservation policy and practice. Traditionally, there has been an extremely limited use of long-term ecological records (greater than 50 years) in biodiversity conservation. There are a number of reasons why such records tend to be discounted, including a perception of poor scale of resolution in both time and space, and the lack of accessibility of long temporal records to non-specialists. Probably more important, however, is the perception that even if suitable temporal records are available, their roles are purely descriptive, simply demonstrating what has occurred before in Earth's history, and are of little use in the actual practice of conservation. This paper asks why this is the case and whether there is a place for the temporal record in conservation management. Key conservation initiatives related to extinctions, identification of regions of greatest diversity/threat, climate change and biological invasions are addressed. Examples of how a temporal record can add information that is of direct practicable applicability to these issues are highlighted. These include (i) the identification of species at the end of their evolutionary lifespan and therefore most at risk from extinction, (ii) the setting of realistic goals and targets for conservation ‘hotspots’, and (iii) the identification of various management tools for the maintenance/restoration of a desired biological state. For climate change conservation strategies, the use of long-term ecological records in testing the predictive power of species envelope models is highlighted, along with the potential of fossil records to examine the impact of sea-level rise. It is also argued that a long-term perspective is essential for the management of biological invasions, not least in determining when an invasive is not an invasive. The paper concludes that often inclusion of a long-term ecological perspective can provide a more scientifically defensible basis for conservation decisions than the one based only on contemporary records. The pivotal issue of this paper is not whether long-term records are of interest to conservation biologists, but how they can actually be utilized in conservation practice and policy.

  • 36.
    Wolf, Jochen B. W.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lindell, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Speciation genetics: current status and evolving approaches Introduction2010In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 365, no 1547, p. 1717-1733Article in journal (Refereed)
    Abstract [en]

    The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues

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