Life Histories and Natural Selection

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PHYSICS AND POLITICS OR THOUGHTS ON THE APPLICATION OF THE PRINCIPLES OF 'NATURAL SELECTION' AND 'INHERITANCE' TO POLITICAL SOCIETY BY WALTER BAGEHOT NEW AND CHEAPER EDITION (also published in the International Scientific Series, crown 8vo. 5s.) CONTENTS. I. THE PRELIMINARY AGE II. THE USE OF CONFLICT III. NATION-MAKING IV. NATION-MAKING V. THE AGE OF DISCUSSION VI. VERIFIABLE PROGRESS POLITICALLY CONSIDERED NO. I. THE PRELIMINARY AGE. One peculiarity of this age is the sudden acquisition of much physical knowledge. There is scarcely a department of science or art which is the same, or at all the same, as it was fifty years ago. A new world of inventions—of railways and of telegraphs— has grown up around us which we cannot help seeing; a new world of ideas is in the air and affects us, though we do not see it. A full estimate of these effects would require a great book, and I am sure I could not write it; but I think I may usefully, in a few papers, show how, upon one or two great points, the new ideas are modifying two old sciences—politics and political economy. Even upon these points my ideas must be incomplete, for the subject is novel; but, at any rate, I may suggest some conclusions, and so show what is requisite even if I do not supply it. If we wanted to describe one of the most marked results, perhaps the most marked result, of late thought, we should say that by it everything is made 'an antiquity.' When, in former times; our ancestors thought of an antiquarian, they described him as occupied with coins, and medals, and Druids' stones; these were then the characteristic records of the decipherable past, and it was with these that decipherers busied themselves. But now there are other relics; indeed, all matter is become such. Science tries to find in each bit of earth the record of the causes which made it precisely what it is; those forces have left their trace, she knows, as much as the tact and hand of the artist left their mark on a classical gem. It would be tedious (and it is not in my way) to reckon up the ingenious questionings by which geology has made part of the earth, at least, tell part of its tale; and the answers would have been meaningless if physiology and conchology and a hundred similar sciences had not brought their aid. Such subsidiary sciences are to the decipherer of the present day what old languages were to the antiquary of other days; they construe for him the words which he discovers, they give a richness and a truth-like complexity to the picture which he paints, even in cases where the particular detail they tell is not much. But what here concerns me is that man himself has, to the eye of science, become 'an antiquity.' She tries to read, is beginning to read, knows she ought to read, in the frame of each man the result of a whole history of all his life, of what he is and what makes him so,—of all his fore-fathers, of what they were and of what made them so. Each nerve has a sort of memory of its past life, is trained or not trained, dulled or quickened, as the case may be; each feature is shaped and characterised, or left loose and meaningless, as may Life Histories and Natural Selection Life Histories and Natural Selection Bởi: OpenStaxCollege A species’ life history describes the series of events over its lifetime, such as how resources are allocated for growth, maintenance, and reproduction Life history traits affect the life table of an organism A species’ life history is genetically determined and shaped by the environment and natural selection Life History Patterns and Energy Budgets Energy is required by all living organisms for their growth, maintenance, and reproduction; at the same time, energy is often a major limiting factor in determining an organism’s survival Plants, for example, acquire energy from the sun via photosynthesis, but must expend this energy to grow, maintain health, and produce energy-rich seeds to produce the next generation Animals have the additional burden of using some of their energy reserves to acquire food Furthermore, some animals must expend energy caring for their offspring Thus, all species have an energy budget: they must balance energy intake with their use of energy for metabolism, reproduction, parental care, and energy storage (such as bears building up body fat for winter hibernation) Parental Care and Fecundity Fecundity is the potential reproductive capacity of an individual within a population In other words, fecundity describes how many offspring could ideally be produced if an individual has as many offspring as possible, repeating the reproductive cycle as soon as possible after the birth of the offspring In animals, fecundity is inversely related to the amount of parental care given to an individual offspring Species, such as many marine invertebrates, that produce many offspring usually provide little if any care for the offspring (they would not have the energy or the ability to so anyway) Most of their energy budget is used to produce many tiny offspring Animals with this strategy are often self-sufficient at a very early age This is because of the energy tradeoff these organisms have made to maximize their evolutionary fitness Because their energy is used for producing offspring instead of parental care, it makes sense that these offspring 1/6 Life Histories and Natural Selection have some ability to be able to move within their environment and find food and perhaps shelter Even with these abilities, their small size makes them extremely vulnerable to predation, so the production of many offspring allows enough of them to survive to maintain the species Animal species that have few offspring during a reproductive event usually give extensive parental care, devoting much of their energy budget to these activities, sometimes at the expense of their own health This is the case with many mammals, such as humans, kangaroos, and pandas The offspring of these species are relatively helpless at birth and need to develop before they achieve self-sufficiency Plants with low fecundity produce few energy-rich seeds (such as coconuts and chestnuts) with each having a good chance to germinate into a new organism; plants with high fecundity usually have many small, energy-poor seeds (like orchids) that have a relatively poor chance of surviving Although it may seem that coconuts and chestnuts have a better chance of surviving, the energy tradeoff of the orchid is also very effective It is a matter of where the energy is used, for large numbers of seeds or for fewer seeds with more energy Early versus Late Reproduction The timing of reproduction in a life history also affects species survival Organisms that reproduce at an early age have a greater chance of producing offspring, but this is usually at the expense of their growth and the maintenance of their health Conversely, organisms that start reproducing later in life often have greater fecundity or are better able to provide parental care, but they risk that they will not survive to reproductive age Examples of this can be seen in fishes Small fish like guppies use their energy to reproduce rapidly, but never attain the size that would give them defense against some predators Larger fish, like the bluegill or shark, use their energy to attain a large size, but so with the risk that they will die before they can reproduce or at least reproduce to their maximum These different energy strategies and tradeoffs are key to understanding the evolution of each species as it maximizes its fitness and fills its niche In terms of energy budgeting, some species “blow it all” and use up most of their energy reserves to reproduce early before they die Other species delay having reproduction to become stronger, more experienced individuals and to make sure that they are strong enough to provide parental care if necessary Single versus Multiple Reproductive Events Some life history traits, such as fecundity, timing of reproduction, and parental care, can be grouped together into general strategies that are used by multiple species Semelparity occurs when a species reproduces ...Super life – how and why ‘cell selection’ leads to the fastest-growing eukaryote Philip Groeneveld 1 , Adriaan H. Stouthamer 1 and Hans V. Westerhoff 1,2,3 1 Department of Molecular Cell Physiology & Mathematical Biochemistry, Netherlands Institute for Systems Biology, Vrije Universiteit, Amsterdam, The Netherlands 2 The Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science, The University of Manchester, UK 3 Swammerdam Institute for Life Sciences, Netherlands Institute for Systems Biology, University of Amsterdam, The Netherlands There is considerable interest in what determines the rate at which reproductive growth occurs. This issue is most intriguing for the ‘maximum’ growth rate (J growth-max ) of the fastest independently replicating organism, relatives of which are used commercially as ‘living factories’. The fastest-dividing organisms are micro-organisms, and we limit our analysis to eukary- otic microbes, as they are most similar to cells of higher organisms. The cell-cycle time of one of the fastest-growing eukaryotes (i.e. a generation time of 70 min [1]) is still seven times longer than that of one of the fastest-growing prokaryotes (i.e. a generation time of < 10 min [2,3]). One of the known fastest- growing microbial eukaryotes is the non-pathogenic industrial yeast Kluyveromyces marxianus, which GRAS status (‘generally recognized as safe’). For these reasons, this organism has been chosen as an efficient vehicle for single-cell protein production [4–7]. In this context, we do not consider early transient cleavage during fast embryonic growth of eukaryotes such as Xenopus laevis [8]. Reproduction in terms of cell number by cleavage is much faster but the net biomass remain constant. Here, we refer to the highest reproduction rate of cells in terms of the maximum specific growth rate (l max ), which is expressed as an increase in net flux of biomass, J growth-rate , per unit of cell mass or total protein, and equals ‘ln 2’ divided by the genera- tion or cell-cycle time. The questions posed in this study also address the minimum cell-cycle time. The maximum (specific) growth rate refers to cellu- lar biosynthesis during which all nutrients are supplied in excess (i.e. substrate-saturated conditions relative to Keywords highest eukaryotic growth rate; modular control analysis; pH-auxostat selection; surface-to-volume ratio optimization; systems biology Correspondence H. V. Westerhoff, The Manchester Centre for Integrative Systems Biology, SCEAS, The University of Manchester, Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7ND, UK Fax: +44 161 306 8918 Tel: +44 161 306 4407 E-mail: Hans.Westerhoff@manchester.ac.uk (Received 20 December 2007, revised 26 October 2008, accepted 3 November 2008) doi:10.1111/j.1742-4658.2008.06778.x What is the highest possible replication rate for living organisms? The cellular growth rate is controlled by a variety of processes. Therefore, it is unclear which metabolic process or group of processes should be activated to increase growth rate. An organism that is already growing fast may already have optimized through evolution all processes that could be opti- mized readily, but may be confronted with a more generic limitation. Here we introduce a method called ‘cell selection’ to select for highest growth rate, and show how such a cellular site of ‘growth control’ was identified. By applying pH-auxostat cultivation to the already fast-growing yeast Kluyveromyces marxianus for a sufficiently long time, we selected a strain with a 30% increased growth rate; its Genome Biology 2008, 9:R69 Open Access 2008Liuet al.Volume 9, Issue 4, Article R69 Research Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective Jinfeng Liu * , Yan Zhang * , Xingye Lei † and Zemin Zhang * Addresses: * Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. † Department of Biostatistics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Correspondence: Zemin Zhang. Email: zemin@gene.com © 2008 Liu et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Measure of selective constraints<p>A large-scale survey using single nucleotide polymorphism data from dbSNP provides insights into the evolutionary selection con-straints on human proteins of different structural and functional categories.</p> Abstract Background: The rates of molecular evolution for protein-coding genes depend on the stringency of functional or structural constraints. The Ka/Ks ratio has been commonly used as an indicator of selective constraints and is typically calculated from interspecies alignments. Recent accumulation of single nucleotide polymorphism (SNP) data has enabled the derivation of Ka/Ks ratios for polymorphism (SNP A/S ratios). Results: Using data from the dbSNP database, we conducted the first large-scale survey of SNP A/ S ratios for different structural and functional properties. We confirmed that the SNP A/S ratio is largely correlated with Ka/Ks for divergence. We observed stronger selective constraints for proteins that have high mRNA expression levels or broad expression patterns, have no paralogs, arose earlier in evolution, have natively disordered regions, are located in cytoplasm and nucleus, or are related to human diseases. On the residue level, we found higher degrees of variation for residues that are exposed to solvent, are in a loop conformation, natively disordered regions or low complexity regions, or are in the signal peptides of secreted proteins. Our analysis also revealed that histones and protein kinases are among the protein families that are under the strongest selective constraints, whereas olfactory and taste receptors are among the most variable groups. Conclusion: Our study suggests that the SNP A/S ratio is a robust measure for selective constraints. The correlations between SNP A/S ratios and other variables provide valuable insights into the natural selection of various structural or functional properties, particularly for human- specific genes and constraints within the human lineage. Background It is well established that there are tremendous variations in rates of evolution among protein-coding genes. A central problem in molecular evolution is to identify factors that determine the rate of protein evolution. One widely accepted principle is that a major force governing the rate of amino acid substitution is the stringency of functional or structural constraints. Proteins with rigorous functional or structural requirements are subject to strong purifying (negative) selec- tive pressure, resulting in smaller numbers of amino acid Published: 8 April 2008 Genome Biology 2008, 9:R69 (doi:10.1186/gb-2008-9-4-r69) Received: 20 March 2008 Revised: 25 March 2008 Accepted: 8 April 2008 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/4/R69 Genome Biology 2008, 9:R69 http://genomebiology.com/2008/9/4/R69 Genome Biology 2008, Volume 9, Issue 4, Article R69 Liu et al. R69.2 changes. Therefore, these proteins tend to evolve slower than proteins with weaker constraints. A classic measure for selec- tive pressure on protein-coding genes is the Ka/Ks ratio [1], http://genomebiology.com/2009/10/7/228 Amasino: Genome Biology 2009, 10:228 Asbtract Recent work in Arabis alpina, a perennial relative of Arabidopsis, has uncovered subtle differences in control of a gene that represses flowering which contributes to the polycarpic habit. There are two extremes of life-history strategies in plants and animals - semelparity and iteroparity [1]. Semelparity is sometimes referred to as the ‘big-bang reproductive strategy’ [2], as semelparous species devote most of their energy and resources to maximizing the number of offspring in a single cycle of reproduction, and die soon after reproducing. Semelparity may be advantageous when the prospects for long-term survival are low. Iteroparous species, in contrast, reproduce multiple times, a strategy that may be advantageous when prospects for long-term survival are good. In the plant kingdom, there are extreme examples of both strategies. At one end of the iteroparous spectrum are redwood trees, which can live for several thousand years with several thousand cycles of reproduction. In contrast, the popular semelparous research model Arabidopsis thaliana can complete its life cycle in less than two months, and once Arabidopsis produces a certain number of off- spring it rapidly senesces and dies, even under optimal growth conditions [3] (Figure 1). Plants that live and reproduce for many years, such as redwoods, are often referred to as perennials. Plants such as Arabidopsis that typically survive only a single growing season are often referred to as annuals. However, the differ ent life-history strategies of plants are better des- cribed by the terms monocarpic (semelparous; reproduces once and dies) and polycarpic (iteroparous; reproduces repeatedly), instead of annual and perennial, respectively. For example, perennial is hard to define, because there are plants that live for many years without flowering and then flower once and die. A striking example is the Haleakalā silversword, Argyroxiphium sandwicense, which may live for more than 50 years before flowering and dying (Figure 1). The molecular basis for the death of monocarpic plants like Arabidopsis after reproduction is not well understood. Plants develop from regions of stem cells called meristems. The shoot apical meristem (SAM) produces cells that differentiate into stems, leaves and flowers. In many monocarpic plants, including Arabidopsis, all active SAMs convert to flower production (that is, become inflorescence meristems). In Arabidopsis, when a certain number of seeds have been produced the inflorescence meristems stop growing, although they do not undergo terminal differ entiation, and the whole plant senesces as the seeds mature [3]. Perhaps inflorescence meristem arrest after repro duction and the subsequent death is a specific genetic program in Arabidopsis, or perhaps the plants simply do not have the energy to sustain further growth from these inflorescence meristems - the plants ‘burn out’ in the effort to produce as many offspring as possible [3]. Thus, a key feature of polycarpy is to maintain a supply of meristems that are capable of vegetative growth; that is, SAMs that can produce shoots with leaves to sustain growth of the plant in future growth cycles. In a recent paper in Nature by Wang et al. [4], the polycarpic habit was studied in a relative of Arabidopsis, Arabis alpina, another member of the family Brassicaceae. A. alpina requires exposure to cold in order to flower (a phenomenon known as vernalization) [5]. However, as expected for a polycarpic plant, vernalization does not result in the flowering of all A. alpina SAMs. Those shoots of A. alpina that do flower cease growth and senesce during seed maturation similarly to shoots of Arabidopsis, but A. alpina maintains a supply of vegetative SAMs for another round of growth. From polycarpy towards monocarpy Wang et al. [4] identified an A. alpina mutant, Ch 22 Warm-Up What you remember about Charles Darwin and his scientific ideas? According to Campbell, what is the definition of “evolution”? Descent with Modification: A Darwinian View of Life Part A: Darwin & Natural Selection What you must know:  How Lamarck’s view of the mechanism of evolution differed from Darwin’s  The role of adaptations, variation, time, reproductive success, and heritability in evolution Descent with Modification Theme:  Evolutionary change is based on the interactions between populations & their environment which results in adaptations (inherited characteristics) to increase fitness Evolution = change over time in the genetic composition of a population Historical Process of Science Aristotle: life-forms arranged on scale on increasing complexity (scala naturae) Aristotle 384-322 B.C Old Testament - Creationism: Earth ~6000 years old; perfect species individually designed by God Natural theology: discovering Creator’s plan by studying nature; to classify nature Carolus Linnaeus 1707-1778 Linnaeus: founder of taxonomy; binomial nomenclature  Domain – Kingdom – Phylum – Class – Order – Family - Genus – Species  (Dear King Philip Came Over For Good Spaghetti)  Domains = Bacteria, Archaea, Eukarya  Classification based on anatomy & morphology Cuvier:  Paleontologist – studied fossils  Deeper strata (layers) - very different fossils from current life  Opposed idea of evolution  Catastrophism – catastrophe destroyed many living species, then repopulated by immigrant species George Cuvier (1769-1832) Hutton / Lyell: Gradualism = geologic change results from slow & gradual, continuous process Uniformitarianism = Earth’s processes same rate in past & present  therefore Earth is very old  Slow & subtle changes in organisms  big change James Hutton 1726-1797 Charles Lyell 1797-1875 Jean-Baptiste Lamarck 1744-1829 Lamarck:  Published theory of evolution (1809)  Use and Disuse: parts of body used  bigger, stronger (eg giraffe’s neck)  Inheritance of Acquired Characteristics: modifications can be passed on  Importance: Recognized that species evolve, although explanation was flawed Malthus:  More babies born than deaths  Consequences of overproducing within environment = war, famine, disease (limits of human pop.)  Struggle for existence Thomas Malthus (1766-1834) Charles Darwin (1809-1882)  English naturalist  1831: joined the HMS Beagle for a 5-year research voyage around the world  Collected and studied plant and animal specimens, bones, fossils  Notable stop: Galapagos Islands HMS Beagle (1831-1836) Galapagos Islands 15 16 Darwin’s Finch Collection The birds were all about the same size, but the shape and size of the beaks of each species were different The vice-governor of the Galapagos Islands told Darwin that he could tell which island a particular tortoise came from by looking at its shell Giant Tortoise 18  Darwin waited 30 years before he published his ideas on evolution  Alfred Russell Wallace – published paper on natural selection first (1858)  Charles Darwin (1859): On the Origin of Species by Means of Natural Selection  Mechanism for evolution is Natural Selection  Darwin didn’t use “evolution”, but rather “descent with modification” 19 “On the Origin of Species by Means of Natural Selection” By Charles Darwin (1859)  Adaptations enhance an organism’s ability to survive and reproduce  Eg Desert fox - large ears, arctic fox - small ears  Overproduction of offspring leads to competition for resources Natural Selection Artificial Selection •Nature decides •“Man” decides •Works on individual •Selective breeding •Inbreeding occurs •eg beaks •eg dalmations Therefore, if humans can create substantial change over short time, nature can over long time Key Ideas of Natural Selection:  Competition for limited resources results in differential survival  Evolutionary Fitness: Individuals with more favorable phenotypes more likely to survive and produce more offspring, and .. .Life Histories and Natural Selection have some ability to be able to move within their environment and find food and perhaps shelter Even with these abilities,... reproductive event, 2/6 Life Histories and Natural Selection sacrificing their health to the point that they not survive Examples of semelparity are bamboo, which flowers once and then dies, and the Chinook... (iteroparity) in its life Review Questions Which of the following is associated with long-term parental care? few offspring many offspring semelparity fecundity A 5/6 Life Histories and Natural Selection