Comparative Structural Models of Similarities and Differences between "Vehicle" and "Target" in Order to Teach Darwinian "Evolution"

ERIC Educational Resources Information Center

Marcelos, Maria Fatima; Nagem, Ronaldo L.

2010-01-01

Our objective is to contribute to the teaching of Classical Darwinian "Evolution" by means of a study of analogies and metaphors. Throughout the history of knowledge about "Evolution" and in Science teaching, tree structures have been used an analogs to refer to "Evolution," such as by Darwin in the "Tree of Life" passage contained in "On The…

Statistical distribution of amino acid sequences: a proof of Darwinian evolution.

PubMed

Eitner, Krystian; Koch, Uwe; Gaweda, Tomasz; Marciniak, Jedrzej

2010-12-01

The article presents results of the listing of the quantity of amino acids, dipeptides and tripeptides for all proteins available in the UNIPROT-TREMBL database and the listing for selected species and enzymes. UNIPROT-TREMBL contains protein sequences associated with computationally generated annotations and large-scale functional characterization. Due to the distinct metabolic pathways of amino acid syntheses and their physicochemical properties, the quantities of subpeptides in proteins vary. We have proved that the distribution of amino acids, dipeptides and tripeptides is statistical which confirms that the evolutionary biodiversity development model is subject to the theory of independent events. It seems interesting that certain short peptide combinations occur relatively rarely or even not at all. First, it confirms the Darwinian theory of evolution and second, it opens up opportunities for designing pharmaceuticals among rarely represented short peptide combinations. Furthermore, an innovative approach to the mass analysis of bioinformatic data is presented. eitner@amu.edu.pl Supplementary data are available at Bioinformatics online.

Darwinian Liberal Education

ERIC Educational Resources Information Center

Arnhart, Larry

2006-01-01

Be it metaphysics, theology, or some other unifying framework, humans have long sought to determine "first principles" underlying knowledge. Larry Arnhart continues in this vein, positing a Darwinian web of genetic, cultural, and cognitive evolution to explain our social behavior in terms of human nature as governed by biology. He leaves it to us…

Darwinian medicine and psoriasis.

PubMed

Romaní de Gabriel, J

2015-04-01

Darwinian medicine, or evolutionary medicine, regards some pathological conditions as attempts by the organism to solve a problem or develop defense mechanisms. At certain stages of human evolution, some diseases may have conferred a selective advantage. Psoriasis is a high-penetrance multigenic disorder with prevalence among whites of up to 3%. Psoriatic lesions have been linked with enhanced wound-healing qualities and greater capacity to fight infection. Leprosy, tuberculosis, and infections caused by viruses similar to human immunodeficiency virus have been postulated as environmental stressors that may have selected for psoriasis-promoting genes in some human populations. The tendency of patients with severe psoriasis to develop metabolic syndrome may reflect the body's attempt to react to environmental stresses and warning signs by triggering insulin resistance and fat storage. Copyright © 2014 Elsevier España, S.L.U. and AEDV. All rights reserved.

Understanding protein evolution: from protein physics to Darwinian selection.

PubMed

Zeldovich, Konstantin B; Shakhnovich, Eugene I

2008-01-01

Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

Getting to Darwin: Obstacles to Accepting Evolution by Natural Selection

NASA Astrophysics Data System (ADS)

Thagard, Paul; Findlay, Scott

2010-06-01

Darwin’s theory of evolution by natural selection is central to modern biology, but is resisted by many people. This paper discusses the major psychological obstacles to accepting Darwin’s theory. Cognitive obstacles to adopting evolution by natural selection include conceptual difficulties, methodological issues, and coherence problems that derive from the intuitiveness of alternative theories. The main emotional obstacles to accepting evolution are its apparent conflict with valued beliefs about God, souls, and morality. We draw on the philosophy of science and on a psychological theory of cognitive and emotional belief revision to make suggestions about what can be done to improve acceptance of Darwinian ideas.

The Mastodon in the room: how Darwinian is neo-Darwinism?

PubMed

Brooks, Daniel R

2011-03-01

Failing to acknowledge substantial differences between Darwinism and neo-Darwinism impedes evolutionary biology. Darwin described evolution as the outcome of interactions between the nature of the organism and the nature of the conditions, each relatively autonomous but both historically and spatially intertwined. Furthermore, he postulated that the nature of the organism was more important than the nature of the conditions, leading to natural selection as an inevitable emergent product of biological systems. The neo-Darwinian tradition assumed a creative rather than selective view of natural selection, with the nature of the organism determined by the nature of the conditions, rendering the nature of the organism and temporal contingency unnecessary. Contemporary advances in biology, specifically the phylogenetics revolution and evo-devo, underscore the significance of history and the nature of the organism in biology. Darwinism explains more biology better, and better resolves apparent anomalies between living systems and more general natural laws, than does neo-Darwinism. The "extended" or "expanded" synthesis currently called for by neo-Darwinians is Darwinism. Copyright © 2010 Elsevier Ltd. All rights reserved.

Mode and tempo in the evolution of socio-political organization: reconciling 'Darwinian' and 'Spencerian' evolutionary approaches in anthropology.

PubMed

Currie, Thomas E; Mace, Ruth

2011-04-12

Traditional investigations of the evolution of human social and political institutions trace their ancestry back to nineteenth century social scientists such as Herbert Spencer, and have concentrated on the increase in socio-political complexity over time. More recent studies of cultural evolution have been explicitly informed by Darwinian evolutionary theory and focus on the transmission of cultural traits between individuals. These two approaches to investigating cultural change are often seen as incompatible. However, we argue that many of the defining features and assumptions of 'Spencerian' cultural evolutionary theory represent testable hypotheses that can and should be tackled within a broader 'Darwinian' framework. In this paper we apply phylogenetic comparative techniques to data from Austronesian-speaking societies of Island South-East Asia and the Pacific to test hypotheses about the mode and tempo of human socio-political evolution. We find support for three ideas often associated with Spencerian cultural evolutionary theory: (i) political organization has evolved through a regular sequence of forms, (ii) increases in hierarchical political complexity have been more common than decreases, and (iii) political organization has co-evolved with the wider presence of hereditary social stratification.

Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life.

PubMed

Arnoldt, Hinrich; Strogatz, Steven H; Timme, Marc

2015-01-01

It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.

The Janus face of Darwinian competition.

PubMed

Hintze, Arend; Phillips, Nathaniel; Hertwig, Ralph

2015-09-10

Without competition, organisms would not evolve any meaningful physical or cognitive abilities. Competition can thus be understood as the driving force behind Darwinian evolution. But does this imply that more competitive environments necessarily evolve organisms with more sophisticated cognitive abilities than do less competitive environments? Or is there a tipping point at which competition does more harm than good? We examine the evolution of decision strategies among virtual agents performing a repetitive sampling task in three distinct environments. The environments differ in the degree to which the actions of a competitor can affect the fitness of the sampling agent, and in the variance of the sample. Under weak competition, agents evolve decision strategies that sample often and make accurate decisions, which not only improve their own fitness, but are good for the entire population. Under extreme competition, however, the dark side of the Janus face of Darwinian competition emerges: Agents are forced to sacrifice accuracy for speed and are prevented from sampling as often as higher variance in the environment would require. Modest competition is therefore a good driver for the evolution of cognitive abilities and of the population as a whole, whereas too much competition is devastating.

Somatic clonal evolution: A selection-centric perspective.

PubMed

Scott, Jacob; Marusyk, Andriy

2017-04-01

It is generally accepted that the initiation and progression of cancers is the result of somatic clonal evolution. Despite many peculiarities, evolution within populations of somatic cells should obey the same Darwinian principles as evolution within natural populations, i.e. variability of heritable phenotypes provides the substrate for context-specific selection forces leading to increased population frequencies of phenotypes, which are better adapted to their environment. Yet, within cancer biology, the more prevalent way to view evolution is as being entirely driven by the accumulation of "driver" mutations. Context-specific selection forces are either ignored, or viewed as constraints from which tumor cells liberate themselves during the course of malignant progression. In this review, we will argue that explicitly focusing on selection forces acting on the populations of neoplastic cells as the driving force of somatic clonal evolution might provide for a more accurate conceptual framework compared to the mutation-centric driver gene paradigm. Whereas little can be done to counteract the "bad luck" of stochastic occurrences of cancer-related mutations, changes in selective pressures and the phenotypic adaptations they induce can, in principle, be exploited to limit the incidence of cancers and to increase the efficiency of existing and future therapies. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. Copyright © 2017 Elsevier B.V. All rights reserved.

The Janus face of Darwinian competition

PubMed Central

Hintze, Arend; Phillips, Nathaniel; Hertwig, Ralph

2015-01-01

Without competition, organisms would not evolve any meaningful physical or cognitive abilities. Competition can thus be understood as the driving force behind Darwinian evolution. But does this imply that more competitive environments necessarily evolve organisms with more sophisticated cognitive abilities than do less competitive environments? Or is there a tipping point at which competition does more harm than good? We examine the evolution of decision strategies among virtual agents performing a repetitive sampling task in three distinct environments. The environments differ in the degree to which the actions of a competitor can affect the fitness of the sampling agent, and in the variance of the sample. Under weak competition, agents evolve decision strategies that sample often and make accurate decisions, which not only improve their own fitness, but are good for the entire population. Under extreme competition, however, the dark side of the Janus face of Darwinian competition emerges: Agents are forced to sacrifice accuracy for speed and are prevented from sampling as often as higher variance in the environment would require. Modest competition is therefore a good driver for the evolution of cognitive abilities and of the population as a whole, whereas too much competition is devastating. PMID:26354182

The relativity of Darwinian populations and the ecology of endosymbiosis.

PubMed

Stencel, Adrian

If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as 'slavery'.

Sexual selection: Another Darwinian process.

PubMed

Gayon, Jean

2010-02-01

the Darwin-Wallace controversy was that most Darwinian biologists avoided the subject of sexual selection until at least the 1950s, Ronald Fisher being a major exception. This controversy still deserves attention from modern evolutionary biologists, because the modern approach inherits from both Darwin and Wallace. The modern approach tends to present sexual selection as a special aspect of the theory of natural selection, although it also recognizes the big difficulties resulting from the inevitable interaction between these two natural processes of selection. And contra Wallace, it considers mate choice as a major process that deserves a proper evolutionary treatment. The paper's conclusion explains why sexual selection can be taken as a test case for a proper assessment of "Darwinism" as a scientific tradition. Darwin's and Wallace's attitudes towards sexual selection reveal two different interpretations of the principle of natural selection: Wallace's had an environmentalist conception of natural selection, whereas Darwin was primarily sensitive to the element of competition involved in the intimate mechanism of any natural process of selection. Sexual selection, which can lack adaptive significance, reveals this exemplarily. 2010 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Alfred Russel Wallace (1823-1913): the forgotten co-founder of the Neo-Darwinian theory of biological evolution.

PubMed

Kutschera, Ulrich; Hossfeld, Uwe

2013-12-01

The British naturalist Alfred Russel Wallace (1823-1913), who had to leave school aged 14 and never attended university, did extensive fieldwork, first in the Amazon River basin (1848-1852) and then in Southeast Asia (1854-1862). Based on this experience, and after reading the corresponding scientific literature, Wallace postulated that species were not created, but are modified descendants of pre-existing varieties (Sarawak Law paper, 1855). Evolution is brought about by a struggle for existence via natural selection, which results in the adaptation of those individuals in variable populations who survive and reproduce (Ternate essay, 1858). In his monograph Darwinism (1889), and in subsequent publications, Wallace extended the contents of Darwin's Origin of Species (1859) into the Neo-Darwinian theory of biological evolution, with reference to the work of August Weismann (1834-1914). Wallace also became the (co)-founder of biogeography, biodiversity research, astrobiology and evolutionary anthropology. Moreover, he envisioned what was later called the anthropocene (i.e., the age of human environmental destructiveness). However, since Wallace believed in atheistic spiritualism and mixed up scientific facts and supernatural speculations in some of his writings, he remains a controversial figure in the history of biology.

What makes Darwinian hydrology "Darwinian"? Asking a different kind of question about landscapes

NASA Astrophysics Data System (ADS)

Harman, C.; Troch, P. A.

2014-02-01

There have been repeated calls for a Darwinian approach to hydrologic science, or for a synthesis of Darwinian and Newtonian approaches, to deepen understanding of the hydrologic system in the larger landscape context, and so develop a better basis for predictions now and in an uncertain future. But what exactly makes a Darwinian approach to hydrology "Darwinian"? While there have now been a number of discussions of Darwinian approaches, many referencing Harte (2002), the term is potentially a source of confusion because its connections to Darwin remain allusive rather than explicit. Here we suggest that the Darwinian approach to hydrology follows the example of Charles Darwin by focusing attention on the patterns of variation in populations and seeking hypotheses that explain these patterns in terms of the mechanisms and conditions that determine their historical development. These hypotheses do not simply catalog patterns or predict them statistically - they connect the present structure with processes operating in the past. Nor are they explanations presented without independent evidence or critical analysis - Darwin's hypotheses about the mechanisms underlying present-day variation could be independently tested and validated. With a Darwinian framework in mind, it is easy to see that a great deal of hydrologic research has already been done that contributes to a Darwinian hydrology - whether deliberately or not. We discuss some practical and philosophical issues with this approach to hydrologic science: how are explanatory hypotheses generated? What constitutes a good hypothesis? How are hypotheses tested? "Historical" sciences - including paleohydrology - have long grappled with these questions, as must a Darwinian hydrologic science. We can draw on Darwin's own example for some answers, though there are ongoing debates about the philosophical nature of his methods and reasoning. Darwin used a range of methods of historical reasoning to develop explanatory

Chemical Evolution and the Evolutionary Definition of Life.

PubMed

Higgs, Paul G

2017-06-01

Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of "just chemistry" and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.

A simple mathematical model of gradual Darwinian evolution: emergence of a Gaussian trait distribution in adaptation along a fitness gradient.

PubMed

Biktashev, Vadim N

2014-04-01

We consider a simple mathematical model of gradual Darwinian evolution in continuous time and continuous trait space, due to intraspecific competition for common resource in an asexually reproducing population in constant environment, while far from evolutionary stable equilibrium. The model admits exact analytical solution. In particular, Gaussian distribution of the trait emerges from generic initial conditions.

The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.

PubMed

Denton, Michael J; Marshall, Craig J; Legge, Michael

2002-12-07

Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form-the celebrated "Laws of Form"-was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.

The Problem with a Darwinian View of Humanity

ERIC Educational Resources Information Center

Cunningham, Paul F.

2009-01-01

Comments on the special issue on Charles Darwin and psychology (Dewsbury, February-March 2009), in which the authors present evidence supporting the validity of Charles Darwin's theory of evolution and how generations of psychologists have viewed the natural world through its light, taking Darwinian theories for granted as being a literal…

Darwinian evolution in the light of genomics

PubMed Central

Koonin, Eugene V.

2009-01-01

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

Directional Darwinian Selection in proteins.

PubMed

McClellan, David A

2013-01-01

Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

Evolution Born of Moisture: Analogies and Parallels Between Anaximander's Ideas on Origin of Life and Man and Later Pre-Darwinian and Darwinian Evolutionary Concepts.

PubMed

Kočandrle, Radim; Kleisner, Karel

2013-01-01

This study focuses on the origin of life as presented in the thought of Anaximander of Miletus but also points to some parallel motifs found in much later conceptions of both the pre-Darwinian German romantic science and post-Darwinian biology. According to Anaximander, life originated in the moisture associated with earth (mud). This moist environment hosted the first living creatures that later populated the dry land. In these descriptions, one can trace the earliest hints of the notion of environmental adaptation. The origin of humans was seen as connected in some way with fish: ancient humans were supposed to have developed inside fish-like animals. Anaximander took into account changes in the development of living creatures (adaptations) and speculated on the origins of humans. Similar ideas are found also in the writings of much later, eighteenth and nineteenth century authors who were close to the tradition of German romantic science. We do not argue that these later concepts are in any way directly linked with those of the pre-Socratics, but they show surprising parallels in, e.g., the hypothesis that life originated in a moist environment or the supposition that human developed from fish-like ancestors. These transformations are seen as a consequence of timeless logic rather than as evolution in historical terms. Despite the accent on the origin of living things, both Anaximander and the later Naturphilosophen lack in their notions the element most characteristic of Darwin's thought, that is, the emphasis on historicity and uniqueness of all that comes into being.

Luria-Delbrück Revisited: The Classic Experiment Doesn't Rule out Lamarckian Evolution

NASA Astrophysics Data System (ADS)

Holmes, Caroline; Ghafari, Mahan; Abbas, Anzar; Saravanan, Varun; Nemenman, Ilya

We re-examine data from the classic 1943 Luria-Delbruck fluctuation experiment. This experiment is often credited with establishing that phage resistance in bacteria is acquired through a Darwinian mechanism (natural selection on standing variation) rather than through a Lamarckian mechanism (environmentally induced mutations). We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms. Analysis of the combined model was not performed in the 1943 paper, and nor was analysis of the possibility of neither model fitting the experiment. Using Bayesian model selection, we find that: 1) all datasets from the paper favor Darwinian over purely Lamarckian evolution, 2) some of the datasets are unable to distinguish between the purely Darwinian and the combined models, and 3) the other datasets cannot be explained by any of the models considered. In summary, the classic experiment cannot rule out Lamarckian contributions to the evolutionary dynamics. This work was supported by National Science Foundation Grant 1410978, NIH training Grant 5R90DA033462, and James S. McDonnell Foundation Grant 220020321.

Origins of Genius: Darwinian Perspectives on Creativity.

ERIC Educational Resources Information Center

Simonton, Dean Keith

This study of creative genius argues that creativity can best be understood as a Darwinian process of variation and selection. The artist or scientist generates a wealth of ideas, and then subjects these ideas to aesthetic or scientific judgment, selecting only those that have the best chance to survive and reproduce. The book draws on the latest…

Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution

NASA Astrophysics Data System (ADS)

Holmes, Caroline M.; Ghafari, Mahan; Abbas, Anzar; Saravanan, Varun; Nemenman, Ilya

2017-10-01

We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper. The Luria-Delbrück paper also did not consider the possibility of neither model fitting the experiment. Using Bayesian model selection, we find that the Luria-Delbrück experiment, indeed, favors the Darwinian evolution over purely Lamarckian. However, our analysis does not rule out the combined model, and hence cannot rule out Lamarckian contributions to the evolutionary dynamics.

Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution.

PubMed

Holmes, Caroline M; Ghafari, Mahan; Abbas, Anzar; Saravanan, Varun; Nemenman, Ilya

2017-08-21

We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper. The Luria-Delbrück paper also did not consider the possibility of neither model fitting the experiment. Using Bayesian model selection, we find that the Luria-Delbrück experiment, indeed, favors the Darwinian evolution over purely Lamarckian. However, our analysis does not rule out the combined model, and hence cannot rule out Lamarckian contributions to the evolutionary dynamics.

In Darwinian evolution, feedback from natural selection leads to biased mutations.

PubMed

Caporale, Lynn Helena; Doyle, John

2013-12-01

Natural selection provides feedback through which information about the environment and its recurring challenges is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The variation upon which natural selection acts is generally described as "random." Yet evidence has been mounting for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and time and independent of the environment or context).  This paper focuses on what is known about the generation and control of mutational variation, emphasizing that it is not uniform across the genome or in time, not unstructured with respect to survival, and is neither memoryless nor independent of the (also far from white) environment. We suggest that, as opposed to frequentist methods, Bayesian analysis could capture the evolution of nonuniform probabilities of distinct classes of mutation, and argue not only that the locations, styles, and timing of real mutations are not correctly modeled as generated by a white noise random process, but that such a process would be inconsistent with evolutionary theory. © 2013 New York Academy of Sciences.

The Malthusian-Darwinian dynamic and the trajectory of civilization

USGS Publications Warehouse

Nekola, Jeffrey C.; Allen, Craig D.; Brown, James H.; Burger, Joseph R.; Davidson, Ana D.; Fristoe, Trevor S.; Hamilton, Marcus J.; Hammond, Sean T.; Kodric-Brown, Astrid; Mercado-Silva, Norman; Okie, Jordan G.

2013-01-01

Two interacting forces influence all populations: the Malthusian dynamic of exponential growth until resource limits are reached, and the Darwinian dynamic of innovation and adaptation to circumvent these limits through biological and/or cultural evolution. The specific manifestations of these forces in modern human society provide an important context for determining how humans can establish a sustainable relationship with the finite Earth.

A good Darwinian? Winwood Reade and the making of a late Victorian evolutionary epic.

PubMed

Hesketh, Ian

2015-06-01

In 1871 the travel writer and anthropologist W. Winwood Reade (1838-1875) was inspired by his correspondence with Darwin to turn his narrow ethnological research on West African tribes into the broadest history imaginable, one that would show Darwin's great principle of natural selection at work throughout the evolutionary history of humanity, stretching back to the origins of the universe itself. But when Martyrdom of Man was published in 1872, Reade confessed that Darwin would not likely find him a very good Darwinian, as he was unable to show that natural selection was anything more than a secondary law that arranges all details. When it came to historicising humans within the sweeping history of all creation, Reade argued that the primary law was that of development, a less contentious theory of human evolution that was better suited to Reade's progressive and teleological history of life. By focussing on the extensive correspondence between Reade and Darwin, this paper reconstructs the attempt to make an explicitly Darwinian evolutionary epic in order to shed light on the moral and aesthetic demands that worked to give shape to Victorian efforts to historicise humans within a vastly expanding timeframe. Copyright © 2015 Elsevier Ltd. All rights reserved.

Darwinian Controversies: An Historiographical Recounting

NASA Astrophysics Data System (ADS)

Depew, David J.

2010-05-01

This essay reviews key controversies in the history of the Darwinian research tradition: the Wilberforce-Huxley debate in 1860, early twentieth-century debates about the heritability of acquired characteristics and the consistency of Mendelian genetics with natural selection; the 1925 Scopes trial about teaching evolution; tensions about race, culture, and eugenics at the 1959 centenary celebration Darwin’s Origin of Species; adaptationism and its critics in the Sociobiology debate of 1970s and, more recently, Evolutionary Psychology; and current disputes about Intelligent Design. These controversies, I argue, are etched into public memory because they occur at the emotionally charged boundaries between public-political, technical-scientific, and personal-religious spheres of discourse. Over most of them falls the shadow of eugenics. The main lesson is that the history of Darwinism cannot be told except by showing the mutual influence of the different norms of discourse that obtain in the personal, technical, and public spheres. Nor can evolutionary biology successfully be taught to citizens and citizens-to-be until the fractious intersections between spheres of discourse have been made explicit. In the course of showing why, I take rival evolutionary approaches to be dynamical historical research traditions rather than static theories. Accordingly, I distinguish Darwin’s version of Darwinism from its later transformations. I pay special attention to the role Darwin assigned to development in evolution, which was marginalized by twentieth-century population genetical Darwinism, but has recently resurfaced in new forms. I also show how the disputed phrases “survival of the fittest” and “social Darwinism” have shaped personal anxieties about “Darwinism,” have provoked public opposition to teaching evolution in public schools, and have cast a shadow over efforts to effectively communicate to the public largely successful technical efforts to make

Evolution of Homospermidine Synthase in the Convolvulaceae: A Story of Gene Duplication, Gene Loss, and Periods of Various Selection Pressures[C][W][OA

PubMed Central

Kaltenegger, Elisabeth; Eich, Eckart; Ober, Dietrich

2013-01-01

Homospermidine synthase (HSS), the first pathway-specific enzyme of pyrrolizidine alkaloid biosynthesis, is known to have its origin in the duplication of a gene encoding deoxyhypusine synthase. To study the processes that followed this gene duplication event and gave rise to HSS, we identified sequences encoding HSS and deoxyhypusine synthase from various species of the Convolvulaceae. We show that HSS evolved only once in this lineage. This duplication event was followed by several losses of a functional gene copy attributable to gene loss or pseudogenization. Statistical analyses of sequence data suggest that, in those lineages in which the gene copy was successfully recruited as HSS, the gene duplication event was followed by phases of various selection pressures, including purifying selection, relaxed functional constraints, and possibly positive Darwinian selection. Site-specific mutagenesis experiments have confirmed that the substitution of sites predicted to be under positive Darwinian selection is sufficient to convert a deoxyhypusine synthase into a HSS. In addition, analyses of transcript levels have shown that HSS and deoxyhypusine synthase have also diverged with respect to their regulation. The impact of protein–protein interaction on the evolution of HSS is discussed with respect to current models of enzyme evolution. PMID:23572540

Obesity: a problem of darwinian proportions?

PubMed

Watnick, Suzanne

2006-10-01

Obesity has been described as an abnormality arising from the evolution of man, who becomes fat during the time of perpetual plenty. From the perspective of "Darwinian Medicine," if famine is avoided, obesity will prevail. Problems regarding obesity arise within many disciplines, including socioeconomic environments, the educational system, science, law, and government. This article will discuss various ethical aspects of several disciplines regarding obesity, with a focus on scientific inquiry. We will discuss this within the categories: (1) chronic kidney disease predialysis, (2) dialysis, and (3) renal transplantation. This article aims to help nephrologists and their patients navigate through the ethical aspects of obesity and chronic kidney disease.

Breeding novel solutions in the brain: a model of Darwinian neurodynamics.

PubMed

Szilágyi, András; Zachar, István; Fedor, Anna; de Vladar, Harold P; Szathmáry, Eörs

2016-01-01

Background : The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods : We combine known components of the brain - recurrent neural networks (acting as attractors), the action selection loop and implicit working memory - to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results : We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns) with hereditary variation and novel variants appear due to (i) noisy recall of patterns from the attractor networks, (ii) noise during transmission of candidate solutions as messages between networks, and, (iii) spontaneously generated, untrained patterns in spurious attractors. Conclusions : Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection) and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.

Genetic variability, individuality and the evolution of the mammalian brain.

PubMed

Lipp, H P

1995-12-01

The neo-Darwinian theory of evolution has difficulty in explaining the rapid evolution of mammalian brain and behavior. I shall argue that the plasticity mechanisms of the brain (i.e., system homeostasis, developmental reorganization, structural adult plasticity, and cognition and learning) have evolved primarily as genetic buffer systems which protect subtle mutations influencing brain structures from natural selection. These buffer systems permit accumulation of genetic variation in the higher system levels of the brain (simply defined as structures with late differentiation), while low-level systems are kept constant by natural selection. The organization of this intrinsic genetic buffering system provides several features facilitating neo-Darwinian evolution: In conclusion, the evolutionary appearance of cognition and intelligence is an ordinary biological mechanism compensating evolutionary drags such as long lifespans and fewer offspring. The concept has heuristic value for identifying gene-brain-behavior relationships and for explaining behavioral consequences of artifical gene deletions.

Aesthetic evolution by mate choice: Darwin's really dangerous idea

PubMed Central

Prum, Richard O.

2012-01-01

Darwin proposed an explicitly aesthetic theory of sexual selection in which he described mate preferences as a ‘taste for the beautiful’, an ‘aesthetic capacity’, etc. These statements were not merely colourful Victorian mannerisms, but explicit expressions of Darwin's hypothesis that mate preferences can evolve for arbitrarily attractive traits that do not provide any additional benefits to mate choice. In his critique of Darwin, A. R. Wallace proposed an entirely modern mechanism of mate preference evolution through the correlation of display traits with male vigour or viability, but he called this mechanism natural selection. Wallace's honest advertisement proposal was stridently anti-Darwinian and anti-aesthetic. Most modern sexual selection research relies on essentially the same Neo-Wallacean theory renamed as sexual selection. I define the process of aesthetic evolution as the evolution of a communication signal through sensory/cognitive evaluation, which is most elaborated through coevolution of the signal and its evaluation. Sensory evaluation includes the possibility that display traits do not encode information that is being assessed, but are merely preferred. A genuinely Darwinian, aesthetic theory of sexual selection requires the incorporation of the Lande–Kirkpatrick null model into sexual selection research, but also encompasses the possibility of sensory bias, good genes and direct benefits mechanisms. PMID:22777014

Aesthetic evolution by mate choice: Darwin's really dangerous idea.

PubMed

Prum, Richard O

2012-08-19

Darwin proposed an explicitly aesthetic theory of sexual selection in which he described mate preferences as a 'taste for the beautiful', an 'aesthetic capacity', etc. These statements were not merely colourful Victorian mannerisms, but explicit expressions of Darwin's hypothesis that mate preferences can evolve for arbitrarily attractive traits that do not provide any additional benefits to mate choice. In his critique of Darwin, A. R. Wallace proposed an entirely modern mechanism of mate preference evolution through the correlation of display traits with male vigour or viability, but he called this mechanism natural selection. Wallace's honest advertisement proposal was stridently anti-Darwinian and anti-aesthetic. Most modern sexual selection research relies on essentially the same Neo-Wallacean theory renamed as sexual selection. I define the process of aesthetic evolution as the evolution of a communication signal through sensory/cognitive evaluation, which is most elaborated through coevolution of the signal and its evaluation. Sensory evaluation includes the possibility that display traits do not encode information that is being assessed, but are merely preferred. A genuinely Darwinian, aesthetic theory of sexual selection requires the incorporation of the Lande-Kirkpatrick null model into sexual selection research, but also encompasses the possibility of sensory bias, good genes and direct benefits mechanisms.

Enquire within: cultural evolution and cognitive science.

PubMed

Heyes, Cecilia

2018-04-05

Cultural evolution and cognitive science need each other. Cultural evolution needs cognitive science to find out whether the conditions necessary for Darwinian evolution are met in the cultural domain. Cognitive science needs cultural evolution to explain the origins of distinctively human cognitive processes. Focusing on the first question, I argue that cultural evolutionists can get empirical traction on third-way cultural selection by rooting the distinction between replication and reconstruction, two modes of cultural inheritance, in the distinction between System 1 and System 2 cognitive processes. This move suggests that cultural epidemiologists are right in thinking that replication has higher fidelity than reconstruction, and replication processes are not genetic adaptations for culture, but wrong to assume that replication is rare. If replication is not rare, an important requirement for third-way cultural selection, one-shot fidelity , is likely to be met. However, there are other requirements, overlooked by dual-inheritance theorists when they conflate strong (Darwinian) and weak (choice) senses of 'cultural selection', including dumb choices and recurrent fidelity In a second excursion into cognitive science, I argue that these requirements can be met by metacognitive social learning strategies , and trace the origins of these distinctively human cognitive processes to cultural evolution. Like other forms of cultural learning, they are not cognitive instincts but cognitive gadgets.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

On the Evolution of Human Language.

ERIC Educational Resources Information Center

Lieberman, Philip

Human linguistic ability depends, in part, on the gradual evolution of man's supralaryngeal vocal tract. The anatomic basis of human speech production is the result of a long evolutionary process in which the Darwinian process of natural selection acted to retain mutations. For auditory perception, the listener operates in terms of the acoustic…

Continuous in vitro evolution of a ribozyme ligase: a model experiment for the evolution of a biomolecule.

PubMed

Ledbetter, Michael P; Hwang, Tony W; Stovall, Gwendolyn M; Ellington, Andrew D

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. In vitro directed evolution (IVDE) frequently serves as a model system for the study of Darwinian evolution but produces noticeable phenotypic shifts in a matter of hours. An IVDE demonstration lab would serve to both directly demonstrate how Darwinian selection can act on a pool of variants and introduce students to an essential method of modern molecular biology. To produce an IVDE demonstration lab, continuous IVDE of a T500 ribozyme ligase population has been paired with a fluorescent strand displacement reporter system to visualize the selection of improved catalytic function. A ribozyme population is taken through rounds of isothermal amplification dependent on the self-ligation of a T7 promoter. As the population is selectively enriched with better ligase activity, the strand displacement system allows for the monitoring of the population's ligation rate. The strand displacement reporter system permits the detection of ligated ribozyme. Once ligated with the T7 promoter, the 5' end of the ribozyme displaces paired fluorophore-quencher oligonucleotides, in turn, generating visible signal upon UV light excitation. As the ligation rate of the population increases, due to the selection for faster ligating species, the fluorescent signal develops more rapidly. The pairing of the continuous isothermal system with the fluorescent reporting scheme allows any user, provided with minimal materials, to model the continuous directed evolution of a biomolecule. Copyright © 2013 Wiley-Liss, Inc.

Darwinian Evolution of Mutualistic RNA Replicators with Different Genes

NASA Astrophysics Data System (ADS)

Mizuuchi, R.; Ichihashi, N.

2017-07-01

We report a sustainable long-term replication and evolution of two distinct cooperative RNA replicators encoding different genes. One of the RNAs evolved to maintain or increase the cooperativity, despite selective advantage of selfish mutations.

Regional selection of the brain size regulating gene CASC5 provides new insight into human brain evolution.

PubMed

Shi, Lei; Hu, Enzhi; Wang, Zhenbo; Liu, Jiewei; Li, Jin; Li, Ming; Chen, Hua; Yu, Chunshui; Jiang, Tianzi; Su, Bing

2017-02-01

Human evolution is marked by a continued enlargement of the brain. Previous studies on human brain evolution focused on identifying sequence divergences of brain size regulating genes between humans and nonhuman primates. However, the evolutionary pattern of the brain size regulating genes during recent human evolution is largely unknown. We conducted a comprehensive analysis of the brain size regulating gene CASC5 and found that in recent human evolution, CASC5 has accumulated many modern human specific amino acid changes, including two fixed changes and six polymorphic changes. Among human populations, 4 of the 6 amino acid polymorphic sites have high frequencies of derived alleles in East Asians, but are rare in Europeans and Africans. We proved that this between-population allelic divergence was caused by regional Darwinian positive selection in East Asians. Further analysis of brain image data of Han Chinese showed significant associations of the amino acid polymorphic sites with gray matter volume. Hence, CASC5 may contribute to the morphological and structural changes of the human brain during recent evolution. The observed between-population divergence of CASC5 variants was driven by natural selection that tends to favor a larger gray matter volume in East Asians.

Darwinian Model Building

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kester, Do; Bontekoe, Romke

2011-03-14

We present a way to generate heuristic mathematical models based on the Darwinian principles of variation and selection in a pool of individuals over many generations. Each individual has a genotype (the hereditary properties) and a phenotype (the expression of these properties in the environment). Variation is achieved by cross-over and mutation operations on the genotype which consists in the present case of a single chromosome. The genotypes 'live' in the environment of the data. Nested Sampling is used to optimize the free parameters of the models given the data, thus giving rise to the phenotypes. Selection is based onmore » the phenotypes.The evidences which naturally follow from the Nested Sampling Algorithm are used in a second level of Nested Sampling to find increasingly better models.The data in this paper originate from the Leiden Cytology and Pathology Laboratory (LCPL), which screens pap smears for cervical cancer. We have data for 1750 women who on average underwent 5 tests each. The data on individual women are treated as a small time series. We will try to estimate the next value of the prime cancer indicator from previous tests of the same woman.« less

Darwinian Model Building

NASA Astrophysics Data System (ADS)

Kester, Do; Bontekoe, Romke

2011-03-01

We present a way to generate heuristic mathematical models based on the Darwinian principles of variation and selection in a pool of individuals over many generations. Each individual has a genotype (the hereditary properties) and a phenotype (the expression of these properties in the environment). Variation is achieved by cross-over and mutation operations on the genotype which consists in the present case of a single chromosome. The genotypes `live' in the environment of the data. Nested Sampling is used to optimize the free parameters of the models given the data, thus giving rise to the phenotypes. Selection is based on the phenotypes. The evidences which naturally follow from the Nested Sampling Algorithm are used in a second level of Nested Sampling to find increasingly better models. The data in this paper originate from the Leiden Cytology and Pathology Laboratory (LCPL), which screens pap smears for cervical cancer. We have data for 1750 women who on average underwent 5 tests each. The data on individual women are treated as a small time series. We will try to estimate the next value of the prime cancer indicator from previous tests of the same woman.

The Darwinian revolution: Rethinking its meaning and significance

PubMed Central

Ruse, Michael

2009-01-01

The Darwinian revolution is generally taken to be one of the key events in the history of Western science. In recent years, however, the very notion of a scientific revolution has come under attack, and in the specific case of Charles Darwin and his Origin of Species there are serious questions about the nature of the change (if there was such) and the specifically Darwinian input. This article considers these issues by addressing these questions: Was there a Darwinian revolution? That is, was there a revolution at all? Was there a Darwinian revolution? That is, what was the specific contribution of Charles Darwin? Was there a Darwinian revolution? That is, what was the conceptual nature of what occurred on and around the publication of the Origin? I argue that there was a major change, both scientifically and in a broader metaphysical sense; that Charles Darwin was the major player in the change, although one must qualify the nature and the extent of the change, looking particularly at things in a broader historical context than just as an immediate event; and that the revolution was complex and we need the insights of rather different philosophies of scientific change to capture the whole phenomenon. In some respects, indeed, the process of analysis is still ongoing and unresolved. PMID:19528652

Corrections to chance fluctuations: quantum mind in biological evolution?

PubMed

Damiani, Giuseppe

2009-01-01

According to neo-Darwinian theory, biological evolution is produced by natural selection of random hereditary variations. This assumption stems from the idea of a mechanical and deterministic world based on the laws of classic physics. However, the increased knowledge of relationships between metabolism, epigenetic systems, and editing of nucleic acids suggests the existence of self-organized processes of adaptive evolution in response to environmental stresses. Living organisms are open thermodynamic systems which use entropic decay of external source of electromagnetic energy to increase their internal dynamic order and to generate new genetic and epigenetic information with a high degree of coherency and teleonomic creativity. Sensing, information processing, and decision making of biological systems might be mainly quantum phenomena. Amplification of microscopic quantum events using the long-range correlation of fractal structures, at the borderline between deterministic order and unpredictable chaos, may be used to direct a reproducible transition of the biological systems towards a defined macroscopic state. The discoveries of many natural genetic engineering systems, the ability to choose the most effective solutions, and the emergence of complex forms of consciousness at different levels confirm the importance of mind-action directed processes in biological evolution, as suggested by Alfred Russel Wallace. Although the main Darwinian principles will remain a crucial component of our understanding of evolution, a radical rethinking of the conceptual structure of the neo-Darwinian theory is needed.

Darwinian algorithms and the Wason selection task: a factorial analysis of social contract selection task problems.

PubMed

Platt, R D; Griggs, R A

1993-08-01

In four experiments with 760 subjects, the present study examined Cosmides' Darwinian algorithm theory of reasoning: specifically, its explanation of facilitation on the Wason selection task. The first experiment replicated Cosmides' finding of facilitation for social contract versions of the selection task, using both her multiple-problem format and a single-problem format. Experiment 2 examined performance on Cosmides' three main social contract problems while manipulating the perspective of the subject and the presence and absence of cost-benefit information. The presence of cost-benefit information improved performance in two of the three problems while the perspective manipulation had no effect. In Experiment 3, the cost-benefit effect was replicated; and performance on one of the three problems was enhanced by the presence of explicit negatives on the NOT-P and NOT-Q cards. Experiment 4 examined the role of the deontic term "must" in the facilitation observed for two of the social contract problems. The presence of "must" led to a significant improvement in performance. The results of these experiments are strongly supportive of social contract theory in that cost-benefit information is necessary for substantial facilitation to be observed in Cosmides' problems. These findings also suggest the presence of other cues that can help guide subjects to a deontic social contract interpretation when the social contract nature of the problem is not clear.

Usefulness of a Darwinian System in a Biotechnological Application: Evolution of Optical Window Fluorescent Protein Variants under Selective Pressure

PubMed Central

Ng, David; Pauli, Jutta; Resch-Genger, Ute; Kühn, Enrico; Heuer, Steffen; Beisker, Wolfgang; Köster, Reinhard W.; Zitzelsberger, Horst; Caldwell, Randolph B

2014-01-01

With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of hypermutation and selection continue until antibodies of high antigen binding specificity emerge (affinity maturation). The avian B cell line DT40, a cell line which is highly amenable to genetic manipulation and exhibits a high rate of targeted integration, utilizes both GC and SHM. Targeting the DT40's diversification machinery onto transgenes of interest inserted into the Ig loci and coupling selective pressure based on the desired outcome mimics evolution. Here we further demonstrate the usefulness of this platform technology by selectively pressuring a large shift in the spectral properties of the fluorescent protein eqFP615 into the highly stable and advanced optical imaging expediting fluorescent protein Amrose. The method is advantageous as it is time and cost effective and no prior knowledge of the outcome protein's structure is necessary. Amrose was evolved to have high excitation at 633 nm and excitation/emission into the far-red, which is optimal for whole-body and deep tissue imaging as we demonstrate in the zebrafish and mouse model. PMID:25192257

Usefulness of a Darwinian system in a biotechnological application: evolution of optical window fluorescent protein variants under selective pressure.

PubMed

Schoetz, Ulrike; Deliolanis, Nikolaos C; Ng, David; Pauli, Jutta; Resch-Genger, Ute; Kühn, Enrico; Heuer, Steffen; Beisker, Wolfgang; Köster, Reinhard W; Zitzelsberger, Horst; Caldwell, Randolph B

2014-01-01

With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of hypermutation and selection continue until antibodies of high antigen binding specificity emerge (affinity maturation). The avian B cell line DT40, a cell line which is highly amenable to genetic manipulation and exhibits a high rate of targeted integration, utilizes both GC and SHM. Targeting the DT40's diversification machinery onto transgenes of interest inserted into the Ig loci and coupling selective pressure based on the desired outcome mimics evolution. Here we further demonstrate the usefulness of this platform technology by selectively pressuring a large shift in the spectral properties of the fluorescent protein eqFP615 into the highly stable and advanced optical imaging expediting fluorescent protein Amrose. The method is advantageous as it is time and cost effective and no prior knowledge of the outcome protein's structure is necessary. Amrose was evolved to have high excitation at 633 nm and excitation/emission into the far-red, which is optimal for whole-body and deep tissue imaging as we demonstrate in the zebrafish and mouse model.

A Scoring Rubric for Students' Responses to Simple Evolution Questions: Darwinian Components

ERIC Educational Resources Information Center

Jensen, Murray; Moore, Randy; Hatch, Jay; Hsu, Leon

2007-01-01

The call to teach students Darwin's theory of evolution by natural selection has been made by a variety of professional organizations. In addition to these national organizations, almost every state has science education guidelines calling for the teaching of evolution. Many administrators and policymakers believe that evolution is being taught,…

Darwinian hydrology: can the methodology Charles Darwin pioneered help hydrologic science?

NASA Astrophysics Data System (ADS)

Harman, C.; Troch, P. A.

2013-05-01

There have been repeated calls for a Darwinian approach to hydrologic science or for a synthesis of Darwinian and Newtonian approaches, to deepen understanding the hydrologic system in the larger landscape context, and so develop a better basis for predictions now and in an uncertain future. But what exactly makes a Darwinian approach to hydrology "Darwinian"? While there have now been a number of discussions of Darwinian approaches, many referencing Harte (2002), the term is potentially a source of confusion while its connections to Darwin remain allusive rather than explicit. Here we discuss the methods that Charles Darwin pioneered to understand a variety of complex systems in terms of their historical processes of change. We suggest that the Darwinian approach to hydrology follows his lead by focusing attention on the patterns of variation in populations, seeking hypotheses that explain these patterns in terms of the mechanisms and conditions that determine their historical development, using deduction and modeling to derive consequent hypotheses that follow from a proposed explanation, and critically testing these hypotheses against new observations. It is not sufficient to catalogue the patterns or predict them statistically. Nor is it sufficient for the explanations to amount to a "just-so" story not subject to critical analysis. Darwin's theories linked present-day variation to mechanisms that operated over history, and could be independently test and falsified by comparing new observations to the predictions of corollary hypotheses they generated. With a Darwinian framework in mind it is easy to see that a great deal of hydrologic research has already been done that contributes to a Darwinian hydrology - whether deliberately or not. The various heuristic methods that Darwin used to develop explanatory theories - extrapolating mechanisms, space for time substitution, and looking for signatures of history - have direct application in hydrologic science. Some

Evolution. A case of system dynamics.

PubMed

Apáthy, Z

1990-01-01

It is contended that the Darwinian theory of evolution is merely a special case of the obsolete Newtonian paradigm. A modern vision of reality, consistent with structuralism in biology, is presented. Some well-known neo-Darwinist explanations of the evolutionary process are quoted accompanied by structuralist interpretations of the same cases. These lead to a different 'mechanism' of evolution, based on internal factors, consistent with contemporary science. It is argued that a great number of specialists who dismiss the Darwinian theory of evolution share a common reason for rejecting it, but differ widely in guessing the motivating factor or factors of evolution.

The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology?

PubMed

Huang, Sui

2012-02-01

The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric 'epigenetic landscape', which actually represents the quasi-potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re-wiring of regulatory interactions - offering a link between genetic mutation and sudden, broad evolutionary changes. Copyright © 2012 WILEY Periodicals, Inc.

The population dynamics of cancer: a Darwinian perspective.

PubMed

Vineis, Paolo; Berwick, Marianne

2006-10-01

Carcinogenesis, at least for some types of cancer, can be interpreted as the consequence of selection of mutated cells similar to what, in the theory of evolution, occurs at the population level. Instead of considering a population of organisms, we can refer to a population of cells belonging to multicellular organisms. Many carcinogens are mutagens, and the observed geographic distribution of cancer is, at least in part, attributable to environmental mutagens. However, the rapid change in risk for some cancers after migration suggests that carcinogenesis involves--in addition to mutations--some late event that most probably consists of the selection of cells already carrying mutations. We review a few examples of such selective pressures: finasteride in prostate cancer, vitamin supplementation in smokers, acquired resistance to chemotherapy, peripheral resistance to insulin, and sunlight and mutations in melanoma. A disease model for such a hypothesis is represented by Paroxysmal Nocturnal Hemoglobinuria (PNH). Mutations can be present at birth, as in the case of PNH, and can have a frequency much higher than the occurrence of the corresponding disease (PNH or lymphocytic leukaemia in children). However, PNH does not require a mutator phenotype, only a mutant phenotype followed by selection. A characteristic feature of cancer, instead, is likely to be the development of the mutator phenotype. We propose a 'Darwinian' model of carcinogenesis. If the model is correct, it suggests that prevention is more complex than avoiding exposure to mutagens. Mutations and genetic instability can be already present at birth. Mutations can be selected in the course of life if they increase survival advantage of the cell under certain environmental circumstances. In addition, gene-environment interactions cannot be interpreted according to a simplified linear model (based on the 'analysis of variance' concept); experimental work suggests that a more comprehensive non

Influences of Teleological and Lamarckian Thinking on Student Understanding of Natural Selection

ERIC Educational Resources Information Center

Stover, Shawn K.; Mabry, Michelle L.

2007-01-01

Previous research has demonstrated creationist, Lamarckian, and teleological reasoning in high school and college students. These lines of thinking conflict with the Darwinian notion of natural selection, which serves as the primary catalyst for biological evolution. The current study assessed evolutionary conceptions in non-science majors,…

Do Galaxies Follow Darwinian Evolution?

NASA Astrophysics Data System (ADS)

2006-12-01

Using VIMOS on ESO's Very Large Telescope, a team of French and Italian astronomers have shown the strong influence the environment exerts on the way galaxies form and evolve. The scientists have for the first time charted remote parts of the Universe, showing that the distribution of galaxies has considerably evolved with time, depending on the galaxies' immediate surroundings. This surprising discovery poses new challenges for theories of the formation and evolution of galaxies. The 'nature versus nurture' debate is a hot topic in human psychology. But astronomers too face similar conundrums, in particular when trying to solve a problem that goes to the very heart of cosmological theories: are the galaxies we see today simply the product of the primordial conditions in which they formed, or did experiences in the past change the path of their evolution? ESO PR Photo 17/06 ESO PR Photo 45/06 Galaxy Distribution in Space In a large, three-year long survey carried out with VIMOS [1], the Visible Imager and Multi-Object Spectrograph on ESO's VLT, astronomers studied more than 6,500 galaxies over a wide range of distances to investigate how their properties vary over different timescales, in different environments and for varying galaxy luminosities [2]. They were able to build an atlas of the Universe in three dimensions, going back more than 9 billion years. This new census reveals a surprising result. The colour-density relation, that describes the relationship between the properties of a galaxy and its environment, was markedly different 7 billion years ago. The astronomers thus found that the galaxies' luminosity, their initial genetic properties, and the environments they reside in have a profound impact on their evolution. "Our results indicate that environment is a key player in galaxy evolution, but there's no simple answer to the 'nature versus nurture' problem in galaxy evolution," said Olivier Le Fèvre from the Laboratoire d'Astrophysique de Marseille

A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution

PubMed Central

Rübben, Albert; Nordhoff, Ole

2013-01-01

Summary Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment. It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution. The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome

A mathematical model of marine bacteriophage evolution.

PubMed

Pagliarini, Silvia; Korobeinikov, Andrei

2018-03-01

To explore how particularities of a host cell-virus system, and in particular host cell replication, affect viral evolution, in this paper we formulate a mathematical model of marine bacteriophage evolution. The intrinsic simplicity of real-life phage-bacteria systems, and in particular aquatic systems, for which the assumption of homogeneous mixing is well justified, allows for a reasonably simple model. The model constructed in this paper is based upon the Beretta-Kuang model of bacteria-phage interaction in an aquatic environment (Beretta & Kuang 1998 Math. Biosci. 149 , 57-76. (doi:10.1016/S0025-5564(97)10015-3)). Compared to the original Beretta-Kuang model, the model assumes the existence of a multitude of viral variants which correspond to continuously distributed phenotypes. It is noteworthy that the model is mechanistic (at least as far as the Beretta-Kuang model is mechanistic). Moreover, this model does not include any explicit law or mechanism of evolution; instead it is assumed, in agreement with the principles of Darwinian evolution, that evolution in this system can occur as a result of random mutations and natural selection. Simulations with a simplistic linear fitness landscape (which is chosen for the convenience of demonstration only and is not related to any real-life system) show that a pulse-type travelling wave moving towards increasing Darwinian fitness appears in the phenotype space. This implies that the overall fitness of a viral quasi-species steadily increases with time. That is, the simulations demonstrate that for an uneven fitness landscape random mutations combined with a mechanism of natural selection (for this particular system this is given by the conspecific competition for the resource) lead to the Darwinian evolution. It is noteworthy that in this system the speed of propagation of this wave (and hence the rate of evolution) is not constant but varies, depending on the current viral fitness and the abundance of susceptible

Five Misunderstandings About Cultural Evolution.

PubMed

Henrich, Joseph; Boyd, Robert; Richerson, Peter J

2008-06-01

Recent debates about memetics have revealed some widespread misunderstandings about Darwinian approaches to cultural evolution. Drawing from these debates, this paper disputes five common claims: (1) mental representations are rarely discrete, and therefore models that assume discrete, gene-like particles (i.e., replicators) are useless; (2) replicators are necessary for cumulative, adaptive evolution; (3) content-dependent psychological biases are the only important processes that affect the spread of cultural representations; (4) the "cultural fitness" of a mental representation can be inferred from its successful transmission; and (5) selective forces only matter if the sources of variation are random. We close by sketching the outlines of a unified evolutionary science of culture.

Evolution and the Growth Process: Natural Selection of Entrepreneurial Traits.

PubMed

Galor, Oded; Michalopoulos, Stelios

2012-03-01

This research suggests that a Darwinian evolution of entrepreneurial spirit played a significant role in the process of economic development and the dynamics of inequality within and across societies. The study argues that entrepreneurial spirit evolved non-monotonically in the course of human history. In early stages of development, risk-tolerant, growth promoting traits generated an evolutionary advantage and their increased representation accelerated the pace of technological progress and the process of economic development. In mature stages of development, however, risk-averse traits gained an evolutionary advantage, diminishing the growth potential of advanced economies and contributing to convergence in economic growth across countries.

The consuming instinct. What Darwinian consumption reveals about human nature.

PubMed

Saad, Gad

2013-01-01

Editor's note: In this engaging talk given last February on a particularly cold and blustery day at Texas Tech University, Professor Gad Saad of Concordia University discusses his work in the area of evolutionary consumption. In making the case for understanding consumerism from a Darwinian perspective, Saad addresses several key tenets from his books The Consuming Instinct (1) and The Evolutionary Bases of Consumption. (2) In particular, Saad argues that: (1) many consumption acts can be mapped onto four key Darwinian modules (survival, mating, kin selection, and reciprocal altruism); and, (2) cultural products such as song lyrics and movie plotlines are fossils of the human mind that highlight a shared, biologically based human nature. In this wide-ranging inquiry, Saad summarizes several of his other empirical works, including the effects of conspicuous consumption on men's testosterone levels (3) and how the ovulatory cycle in the human female influences consumption. (4) Overall, Professor Saad contends that an infusion of evolutionary and biologically based perspectives into the discipline of consumer behavior and related government regulatory policies yields myriad benefits, notably greater consilience, more effective practices, an ethos of interdisciplinarity, and methodological pluralism.

Evolution by epigenesis: farewell to Darwinism, neo- and otherwise.

PubMed

Balon, Eugene K

2004-01-01

In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. The critics advanced other theories instead of 'natural selection' and the survival of the fittest'. 'Saltatory ontogeny' and 'epigenesis' are such new theories proposed to explain how variations in ontogeny and novelties in evolution are created. They are reviewed again in the present essay that also tries to explain how Darwinians, artificially kept dominant in academia and in granting agencies, are preventing their acceptance. Epigenesis, the mechanism of ontogenies, creates in every generation alternative variations in a saltatory way that enable the organisms to survive in the changing environments as either altricial or precocial forms. The constant production of two such forms and their survival in different environments makes it possible, over a sequence of generations, to introduce changes and establish novelties--the true phenomena of evolution. The saltatory units of evolution remain far-from-stable structures capable of self-organization and self-maintenance (autopoiesis).

Evolution and the Growth Process: Natural Selection of Entrepreneurial Traits*

PubMed Central

Galor, Oded; Michalopoulos, Stelios

2013-01-01

This research suggests that a Darwinian evolution of entrepreneurial spirit played a significant role in the process of economic development and the dynamics of inequality within and across societies. The study argues that entrepreneurial spirit evolved non-monotonically in the course of human history. In early stages of development, risk-tolerant, growth promoting traits generated an evolutionary advantage and their increased representation accelerated the pace of technological progress and the process of economic development. In mature stages of development, however, risk-averse traits gained an evolutionary advantage, diminishing the growth potential of advanced economies and contributing to convergence in economic growth across countries. PMID:25089059

Contributions of experimental protobiogenesis to the theory of evolution

NASA Technical Reports Server (NTRS)

Fox, S. W.

1976-01-01

Inferences from experiments in protobiogenesis are examined as a forward extension of the theory of evolutionary biology. A nondiscontinuous, intraconsistent theory of general evolution embracing both protobiology and biology is outlined. This overview emphasizes Darwinian selection in the later stages of evolution, and stereochemical molecular selection in some of its earlier stages. It incorporates the concept of limitation of the scope of evolution by internal constraints on variation, based on the argument that internally limiting constraints observed in experiments with molecules are operative in organisms, if chemical processes occur within biological processes and biological processes are assumed to be exponentializations of chemical processes. Major evolutionary events might have occurred by rapid self-assembly processes analogous to those observed in the formation of phase-separated microspheres from amorphous powder or supersaturated solutions.

Modelling Evolution and SETI Mathematically

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2012-05-01

Darwinian evolution theory may be regarded as a part of SETI theory in that the factor fl in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor fl is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factor increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions constrained between the time axis and the exponential growth curve. Finally, since each lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

Was there a Darwinian Revolution? Yes, no, and maybe!

PubMed

Ruse, Michael

2014-01-01

Was there a Darwinian Revolution and was it but part of the Scientific Revolution? Before Thomas Kuhn's Structure of Scientific Revolutions in 1962, most people thought that there was a Darwinian Revolution, that it was in some sense connected to the Scientific Revolution, but that neither question nor answer was terribly interesting. Then revolutions in science became a matter of intense debate, not so much about their very existence but about their nature. Was there a switch in world-views? Did the facts change? What was the importance of social groups? And so forth. Recently however some students of the history of science have started to argue that the very questions are misconceived and that there cannot have been a Darwinian Revolution and its relationship to the Scientific Revolution is imaginary because there are no such revolutions in science! This paper takes a sympathetic look at these issues, concluding that there is still life in the revolution-in-science issue, that Kuhn's book was seminal and still has things of importance to say, but that matters are more complex and more interesting than we thought back then. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process.

PubMed

Wu, Chung-I; Wang, Hurng-Yi; Ling, Shaoping; Lu, Xuemei

2016-11-23

Although tumorigenesis has been accepted as an evolutionary process ( 20 , 102 ), many forces may operate differently in cancers than in organisms, as they evolve at vastly different time scales. Among such forces, natural selection, here defined as differential cellular proliferation among distinct somatic cell genotypes, is particularly interesting because its action might be thwarted in multicellular organisms ( 20 , 29 ). In this review, selection is analyzed in two stages of cancer evolution: Stage I is the evolution between tumors and normal tissues, and Stage II is the evolution within tumors. The Cancer Genome Atlas (TCGA) data show a low degree of convergent evolution in Stage I, where genetic changes are not extensively shared among cases. An equally important, albeit much less highlighted, discovery using TCGA data is that there is almost no net selection in cancer evolution. Both positive and negative selection are evident but they neatly cancel each other out, rendering total selection ineffective in the absence of recombination. The efficacy of selection is even lower in Stage II, where neutral (non-Darwinian) evolution is increasingly supported by high-density sampling studies ( 81 , 123 ). Because natural selection is not a strong deterministic force, cancers usually evolve divergently even in similar tissue environments.

Darwin, artificial selection, and poverty.

PubMed

Sanchez, Luis

2010-03-01

This paper argues that the processes of evolutionary selection are becoming increasingly artificial, a trend that goes against the belief in a purely natural selection process claimed by Darwin's natural selection theory. Artificial selection is mentioned by Darwin, but it was ignored by Social Darwinists, and it is all but absent in neo-Darwinian thinking. This omission results in an underestimation of probable impacts of artificial selection upon assumed evolutionary processes, and has implications for the ideological uses of Darwin's language, particularly in relation to poverty and other social inequalities. The influence of artificial selection on genotypic and phenotypic adaptations arguably represents a substantial shift in the presumed path of evolution, a shift laden with both biological and political implications.

Universal statistics of selected values

NASA Astrophysics Data System (ADS)

Smerlak, Matteo; Youssef, Ahmed

2017-03-01

Selection, the tendency of some traits to become more frequent than others under the influence of some (natural or artificial) agency, is a key component of Darwinian evolution and countless other natural and social phenomena. Yet a general theory of selection, analogous to the Fisher-Tippett-Gnedenko theory of extreme events, is lacking. Here we introduce a probabilistic definition of selection and show that selected values are attracted to a universal family of limiting distributions which generalize the log-normal distribution. The universality classes and scaling exponents are determined by the tail thickness of the random variable under selection. Our results provide a possible explanation for skewed distributions observed in diverse contexts where selection plays a key role, from molecular biology to agriculture and sport.

Synthetic genetic polymers capable of heredity and evolution.

PubMed

Pinheiro, Vitor B; Taylor, Alexander I; Cozens, Christopher; Abramov, Mikhail; Renders, Marleen; Zhang, Su; Chaput, John C; Wengel, Jesper; Peak-Chew, Sew-Yeu; McLaughlin, Stephen H; Herdewijn, Piet; Holliger, Philipp

2012-04-20

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

Why mental disorders are just mental dysfunctions (and nothing more): some Darwinian arguments.

PubMed

De Block, Andreas

2008-09-01

Mental disorders are often thought to be harmful dysfunctions. Jerome Wakefield has argued that such dysfunctions should be understood as failures of naturally selected functions. This suggests, implicitly, that evolutionary biology and other Darwinian disciplines hold important information for anyone working on answering the philosophical question, 'what is a mental disorder?'. In this article, the author argues that Darwinian theory is not only relevant to the understanding of the disrupted functions, but it also sheds light on the disruption itself, as well as on the harm that attends the disruption. The arguments advanced here are partially based on the view that a core feature of Darwinism is that it stresses the environmental relativity of functions and dysfunctions. These arguments show a very close empirical connection between social judgments (values) and dysfunctions (psychopathology), which is of interest for psychiatric theory. Philosophically, they lead to the conclusion that the concept of mental disorder is identical to the concept of mental dysfunction. Consequently, it is both misleading and redundant to conceptualize mental disorders as 'harmful dysfunctions', and not simply as 'mental dysfunctions'.

The physics of evolution

NASA Astrophysics Data System (ADS)

Eigen, Manfred

1988-12-01

The Darwinian concept of evolution through natural selection has been revised and put on a solid physical basis, in a form which applies to self-replicable macromolecules. Two new concepts are introduced: sequence space and quasi-species. Evolutionary change in the DNA- or RNA-sequence of a gene can be mapped as a trajectory in a sequence space of dimension ν, where ν corresponds to the number of changeable positions in the genomic sequence. Emphasis, however, is shifted from the single surviving wildtype, a single point in the sequence space, to the complex structure of the mutant distribution that constitutes the quasi-species. Selection is equivalent to an establishment of the quasi-species in a localized region of sequence space, subject to threshold conditions for the error rate and sequence length. Arrival of a new mutant may violate the local threshold condition and thereby lead to a displacement of the quasi-species into a different region of sequence space. This transformation is similar to a phase transition; the dynamical equations that describe the quase-species have been shown to be analogous to those of the two-dimensional Ising model of ferromagnetism. The occurrence of a selectively advantageous mutant is biased by the particulars of the quasi-species distribution, whose mutants are populated according to their fitness relative to that of the wild-type. Inasmuch as fitness regions are connected (like mountain ridges) the evolutionary trajectory is guided to regions of optimal fitness. Evolution experiments in test tubes confirm this modification of the simple chance and law nature of the Darwinian concept. The results of the theory can also be applied to the construction of a machine that provides optimal conditions for a rapid evolution of functionally active macromolecules. An introduction to the physics of molecular evolution by the author has appeared recently.1 Detailed studies of the kinetics and mechanisms of replication of RNA, the most

Evolution and stability of altruist strategies in microbial games

NASA Astrophysics Data System (ADS)

Adami, Christoph; Schossau, Jory; Hintze, Arend

2012-01-01

When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory (EGT). We study the predictions of EGT for the bacterial “suicide bomber” game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

A Mathematical Model for Evolution and SETI

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2011-12-01

Darwinian evolution theory may be regarded as a part of SETI theory in that the factor fl in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor fl is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factors increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions (b-lognormals) constrained between the time axis and the exponential growth curve. Finally, since each b-lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

A Model of Social Selection and Successful Altruism

DTIC Science & Technology

1989-10-07

D., The evolution of social behavior. Annual Reviews of Ecological Systems, 5:325-383 (1974). 2. Dawkins , R., The selfish gene . Oxford: Oxford...alive and well. it will be important to re- examine this striking historical experience,-not in terms o, oversimplified models of the " selfish gene ," but...Darwinian Analysis The acceptance by many modern geneticists of the axiom that the basic unit of selection Is the " selfish gene " quickly led to the

The statesman and the ophthalmologist: Gladstone and Magnus on the evolution of human colour vision, one small episode of the nineteenth-century Darwinian debate.

PubMed

Bellmer, E H

1999-01-01

Among the numerous nineteenth-century sorties into particular aspects of the Darwinian debate are two 1877 publications. The first, Die Geschichtliche Entwickelung des Farbensinnes, was a treatise on the evolutionary development of human colour vision by Hugo Magnus, an obscure German ophthalmologist. The other, The Colour-Sense, was an article by William Ewart Gladstone, the great British statesman. Magnus, working from linguistic science and optical physiology, developed the theory that humankind had passed through successive stages of colour recognition, from none to full perception, brightest colours first. Gladstone supported the theory with data from his studies of Homeric colour words, placing Homer at a very early stage. Their theory was not accepted. It assumed colour vocabulary to be an index of colour recognition, and too little was known about the nature or age of early man. The present study intends to follow this particular episode as an excellent example of the scholarship, argumentation, and limited scientific knowledge of the time, as applied to human evolution.

Darwinism and ethology. The role of natural selection in animals and humans.

PubMed

Gervet, J; Soleilhavoup, M

1997-11-01

The role of behaviour in biological evolution is examined within the context of Darwinism. All Darwinian models are based on the distinction of two mechanisms: one that permits faithful transmission of a feature from one generation to another, and another that differentially regulates the degree of this transmission. Behaviour plays a minimal role as an agent of transmission in the greater part of the animal kingdom; by contrast, the forms it may assume strongly influence the mechanisms of selection regulating the different rates of transmission. We consider the decisive feature of the human species to be the existence of a phenotypical system of cultural coding characterized by precision and reliability which are the distinctive feature of genetic coding in animals. We examine the consequences for the application of the Darwinian model to human history.

Quantitative Imaging in Cancer Evolution and Ecology

PubMed Central

Grove, Olya; Gillies, Robert J.

2013-01-01

Cancer therapy, even when highly targeted, typically fails because of the remarkable capacity of malignant cells to evolve effective adaptations. These evolutionary dynamics are both a cause and a consequence of cancer system heterogeneity at many scales, ranging from genetic properties of individual cells to large-scale imaging features. Tumors of the same organ and cell type can have remarkably diverse appearances in different patients. Furthermore, even within a single tumor, marked variations in imaging features, such as necrosis or contrast enhancement, are common. Similar spatial variations recently have been reported in genetic profiles. Radiologic heterogeneity within tumors is usually governed by variations in blood flow, whereas genetic heterogeneity is typically ascribed to random mutations. However, evolution within tumors, as in all living systems, is subject to Darwinian principles; thus, it is governed by predictable and reproducible interactions between environmental selection forces and cell phenotype (not genotype). This link between regional variations in environmental properties and cellular adaptive strategies may permit clinical imaging to be used to assess and monitor intratumoral evolution in individual patients. This approach is enabled by new methods that extract, report, and analyze quantitative, reproducible, and mineable clinical imaging data. However, most current quantitative metrics lack spatialness, expressing quantitative radiologic features as a single value for a region of interest encompassing the whole tumor. In contrast, spatially explicit image analysis recognizes that tumors are heterogeneous but not well mixed and defines regionally distinct habitats, some of which appear to harbor tumor populations that are more aggressive and less treatable than others. By identifying regional variations in key environmental selection forces and evidence of cellular adaptation, clinical imaging can enable us to define intratumoral

A mathematical model for evolution and SETI.

PubMed

Maccone, Claudio

2011-12-01

Darwinian evolution theory may be regarded as a part of SETI theory in that the factor f(l) in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor f(l) is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factors increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions (b-lognormals) constrained between the time axis and the exponential growth curve. Finally, since each b-lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

Evolution and complexity: the double-edged sword.

PubMed

Miconi, Thomas

2008-01-01

We attempt to provide a comprehensive answer to the question of whether, and when, an arrow of complexity emerges in Darwinian evolution. We note that this expression can be interpreted in different ways, including a passive, incidental growth, or a pervasive bias towards complexification. We argue at length that an arrow of complexity does indeed occur in evolution, which can be most reasonably interpreted as the result of a passive trend rather than a driven one. What, then, is the role of evolution in the creation of this trend, and under which conditions will it emerge? In the later sections of this article we point out that when certain proper conditions (which we attempt to formulate in a concise form) are met, Darwinian evolution predictably creates a sustained trend of increase in maximum complexity (that is, an arrow of complexity) that would not be possible without it; but if they are not, evolution will not only fail to produce an arrow of complexity, but may actually prevent any increase in complexity altogether. We conclude that, with regard to the growth of complexity, evolution is very much a double-edged sword.

Prebiological evolution and the metabolic origins of life.

PubMed

Pratt, Andrew J

2011-01-01

The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution.

The sexual cascade and the rise of pre-ejaculatory (Darwinian) sexual selection, sex roles, and sexual conflict.

PubMed

Parker, Geoff A

2014-08-21

After brief historic overviews of sexual selection and sexual conflict, I argue that pre-ejaculatory sexual selection (the form of sexual selection discussed by Darwin) arose at a late stage in an inevitable succession of transitions flowing from the early evolution of syngamy to the evolution of copulation and sex roles. If certain conditions were met, this "sexual cascade" progressed inevitably, if not, sexual strategy remained fixed at a given stage. Prolonged evolutionary history of intense sperm competition/selection under external fertilization preceded the rise of advanced mobility, which generated pre-ejaculatory sexual selection, followed on land by internal fertilization and reduced sperm competition in the form of postcopulatory sexual selection. I develop a prospective model of the early evolution of mobility, which, as Darwin realized, was the catalyst for pre-ejaculatory sexual selection. Stages in the cascade should be regarded as consequential rather than separate phenomena and, as such, invalidate much current opposition to Darwin-Bateman sex roles. Potential for sexual conflict occurs throughout, greatly increasing later in the cascade, reaching its peak under precopulatory sexual selection when sex roles become highly differentiated. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

The Sexual Cascade and the Rise of Pre-Ejaculatory (Darwinian) Sexual Selection, Sex Roles, and Sexual Conflict

PubMed Central

Parker, Geoff A.

2014-01-01

After brief historic overviews of sexual selection and sexual conflict, I argue that pre-ejaculatory sexual selection (the form of sexual selection discussed by Darwin) arose at a late stage in an inevitable succession of transitions flowing from the early evolution of syngamy to the evolution of copulation and sex roles. If certain conditions were met, this “sexual cascade” progressed inevitably, if not, sexual strategy remained fixed at a given stage. Prolonged evolutionary history of intense sperm competition/selection under external fertilization preceded the rise of advanced mobility, which generated pre-ejaculatory sexual selection, followed on land by internal fertilization and reduced sperm competition in the form of postcopulatory sexual selection. I develop a prospective model of the early evolution of mobility, which, as Darwin realized, was the catalyst for pre-ejaculatory sexual selection. Stages in the cascade should be regarded as consequential rather than separate phenomena and, as such, invalidate much current opposition to Darwin–Bateman sex roles. Potential for sexual conflict occurs throughout, greatly increasing later in the cascade, reaching its peak under precopulatory sexual selection when sex roles become highly differentiated. PMID:25147177

Adaptation, teleology, and selection by consequences

PubMed Central

Ringen, Jon D.

1993-01-01

This paper presents and defends the view that reinforcement and natural selection are selection processes, that selection processes are neither mechanistic nor teleological, and that mentalistic and vitalistic processes are teleological but not mechanistic. The differences between these types of processes are described and used in discussing the conceptual and methodological significance of “selection type theories” and B. F. Skinner's radical behaviorist view that “operant behavior is the field of intention, purpose, and expectation. It deals with that field precisely as the theory of evolution has dealt with another kind of purpose” (1986, p. 716). The antimentalism of radical behaviorism emerges as a post-Darwinian extension of Francis Bacon's (and Galileo's) influential view that “[the introduction of final causes] rather corrupts than advances the sciences” (Bacon, 1905, p. 302). PMID:16812698

Just like the rest of evolution in Mother Nature, the evolution of cancers may be driven by natural selection, and not by haphazard mutations

PubMed Central

Zhang, Ju; Lou, Xiaomin; Zellmer, Lucas; Liu, Siqi; Xu, Ningzhi; Liao, D. Joshua

2014-01-01

Sporadic carcinogenesis starts from immortalization of a differentiated somatic cell or an organ-specific stem cell. The immortalized cell incepts a new or quasinew organism that lives like a parasite in the patient and usually proceeds to progressive simplification, constantly engendering intermediate organisms that are simpler than normal cells. Like organismal evolution in Mother Nature, this cellular simplification is a process of Darwinian selection of those mutations with growth- or survival-advantages, from numerous ones that occur randomly and stochastically. Therefore, functional gain of growth- or survival-sustaining oncogenes and functional loss of differentiation-sustaining tumor suppressor genes, which are hallmarks of cancer cells and contribute to phenotypes of greater malignancy, are not drivers of carcinogenesis but are results from natural selection of advantageous mutations. Besides this mutation-load dependent survival mechanism that is evolutionarily low and of an asexual nature, cancer cells may also use cell fusion for survival, which is an evolutionarily-higher mechanism and is of a sexual nature. Assigning oncogenes or tumor suppressor genes or their mutants as drivers to induce cancer in animals may somewhat coerce them to create man-made oncogenic pathways that may not really be a course of sporadic cancer formations in the human. PMID:25594068

The instinctual nation-state: non-Darwinian theories, state science and ultra-nationalism in Oka Asajirō's Evolution and Human Life.

PubMed

Sullivan, Gregory

2011-01-01

In his anthology of socio-political essays, Evolution and Human Life, Oka Asajirō (1868-1944), early twentieth century Japan's foremost advocate of evolutionism, developed a biological vision of the nation-state as super-organism that reflected the concerns and aims of German-inspired Meiji statism and anticipated aspects of radical ultra-nationalism. Drawing on non-Darwinian doctrines, Oka attempted to realize such a fused or organic state by enhancing social instincts that would bind the minzoku (ethnic nation) and state into a single living entity. Though mobilization during the Russo-Japanese War seemed to evince this super-organism, the increasingly contentious and complex society that emerged in the war's aftermath caused Oka to turn first to Lamarckism and eventually to orthogenesis in the hopes of preserving the instincts needed for a viable nation-state. It is especially in the state interventionist measures that Oka finally came to endorse in order to forestall orthogenetically-driven degeneration that the technocratic proclivities of his statist orientation become most apparent. The article concludes by suggesting that Oka's emphasis on degeneration, autarkic expansion, and, most especially, totalitarian submersion of individuals into the statist collectivity indicates a complex relationship between his evolutionism and fascist ideology, what recent scholarship has dubbed radical Shinto ultra-nationalism.

Constructive neutral evolution: exploring evolutionary theory's curious disconnect.

PubMed

Stoltzfus, Arlin

2012-10-13

Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article.

Teaching Evolution: A Heuristic Study of Personal and Cultural Dissonance

ERIC Educational Resources Information Center

Grimes, Larry G.

2012-01-01

Darwinian evolution is a robustly supported scientific theory. Yet creationists continue to challenge its teaching in American public schools. Biology teachers in all 50 states are responsible for teaching science content standards that include evolution. As products of their backgrounds and affiliations teachers bring personal attitudes and…

Warfare, genocide, and ethnic conflict: a Darwinian approach.

PubMed

Dimijian, Gregory G

2010-07-01

As the 21st century dawns, I reflect on the history of humankind with growing concern about the need to understand the underlying biological and cultural roots of ethnic conflict and warfare. In the many studies of human conflict, innate biological predispositions have been neglected. This article is the third part of a series of seminars for medical residents at the University of Texas Southwestern Medical School at Dallas (see http://adarwinstudygroup.org/). The series starts with in-depth coverage of Darwinian natural and sexual selection, with examples from the domestication of animals and plants and the crisis of antibiotic resistance. The series strives to show how biology has been neglected in the study of the we-they orientation of human behavior, with its devastating consequences. The subject material is profoundly disturbing, as it looks at "human nature" and contrasts the "dark side" of human behavior with the opposite, profoundly caring and loving side.

Warfare, genocide, and ethnic conflict: a Darwinian approach

PubMed Central

2010-01-01

As the 21st century dawns, I reflect on the history of humankind with growing concern about the need to understand the underlying biological and cultural roots of ethnic conflict and warfare. In the many studies of human conflict, innate biological predispositions have been neglected. This article is the third part of a series of seminars for medical residents at the University of Texas Southwestern Medical School at Dallas (see http://adarwinstudygroup.org/). The series starts with in-depth coverage of Darwinian natural and sexual selection, with examples from the domestication of animals and plants and the crisis of antibiotic resistance. The series strives to show how biology has been neglected in the study of the we-they orientation of human behavior, with its devastating consequences. The subject material is profoundly disturbing, as it looks at “human nature” and contrasts the “dark side” of human behavior with the opposite, profoundly caring and loving side. PMID:21240320

Evolution of Genes Involved in Gamete Interaction: Evidence for Positive Selection, Duplications and Losses in Vertebrates

PubMed Central

Callebaut, Isabelle; Laurin, Michel; Pascal, Géraldine; Poupon, Anne; Goudet, Ghylène; Monget, Philippe

2012-01-01

Genes encoding proteins involved in sperm-egg interaction and fertilization exhibit a particularly fast evolution and may participate in prezygotic species isolation [1], [2]. Some of them (ZP3, ADAM1, ADAM2, ACR and CD9) have individually been shown to evolve under positive selection [3], [4], suggesting a role of positive Darwinian selection on sperm-egg interaction. However, the genes involved in this biological function have not been systematically and exhaustively studied with an evolutionary perspective, in particular across vertebrates with internal and external fertilization. Here we show that 33 genes among the 69 that have been experimentally shown to be involved in fertilization in at least one taxon in vertebrates are under positive selection. Moreover, we identified 17 pseudogenes and 39 genes that have at least one duplicate in one species. For 15 genes, we found neither positive selection, nor gene copies or pseudogenes. Genes of teleosts, especially genes involved in sperm-oolemma fusion, appear to be more frequently under positive selection than genes of birds and eutherians. In contrast, pseudogenization, gene loss and gene gain are more frequent in eutherians. Thus, each of the 19 studied vertebrate species exhibits a unique signature characterized by gene gain and loss, as well as position of amino acids under positive selection. Reflecting these clade-specific signatures, teleosts and eutherian mammals are recovered as clades in a parsimony analysis. Interestingly the same analysis places Xenopus apart from teleosts, with which it shares the primitive external fertilization, and locates it along with amniotes (which share internal fertilization), suggesting that external or internal environmental conditions of germ cell interaction may not be the unique factors that drive the evolution of fertilization genes. Our work should improve our understanding of the fertilization process and on the establishment of reproductive barriers, for example by

Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern

PubMed Central

2012-01-01

Background The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages. Results We sequenced psbA , which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them. Conclusions The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA , in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study

Directed Evolution as a Powerful Synthetic Biology Tool

PubMed Central

Cobb, Ryan E.; Sun, Ning; Zhao, Huimin

2012-01-01

At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels. PMID:22465795

Evolution: like any other science it is predictable.

PubMed

Morris, Simon Conway

2010-01-12

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology ('evolution explains evolution'). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.

Evolution of the Creative Mind.

ERIC Educational Resources Information Center

Lumsden, Charles J.; Findlay, C. Scott

1988-01-01

A model of the Darwinian evolution of creative thinking is proposed. Creative thinking is modeled as a re-linkage of connections among mental representations, occurring in relationship to gene-culture heterarchy, which is a system of causative and motivational connections among the individual, the innate regularities of cognitive development, and…

From Darwinian to technological evolution: forgetting the human lottery.

PubMed

Tintino, Giorgio

2014-01-01

The GRIN technologies (-geno, -robo, -info, -nano) promise to change the inner constitution of human body and its own existence. This transformation involves the structure of our lives and represent a brave new world that we have to explore and to manage. In this sense, the traditional tools of humanism seems very inadequate to think the biotech century and there is a strong demand of a new thought for the evolution and the concrete history of life. The posthuman philosophy tries to take this new path of human existence in all of its novelty since GRIN technologies seem to promise new and unexpected paths of evolution to living beings and, above all, man. For this, the post-human thought, as we see, is a new anthropological overview on the concrete evolution of human being, an overview that involves an epistemological revolution of the categories that humanism uses to conceptualize the journey that divides the Homo sapiens from the man. But, is this right?

Life cycles, fitness decoupling and the evolution of multicellularity.

PubMed

Hammerschmidt, Katrin; Rose, Caroline J; Kerr, Benjamin; Rainey, Paul B

2014-11-06

Cooperation is central to the emergence of multicellular life; however, the means by which the earliest collectives (groups of cells) maintained integrity in the face of destructive cheating types is unclear. One idea posits cheats as a primitive germ line in a life cycle that facilitates collective reproduction. Here we describe an experiment in which simple cooperating lineages of bacteria were propagated under a selective regime that rewarded collective-level persistence. Collectives reproduced via life cycles that either embraced, or purged, cheating types. When embraced, the life cycle alternated between phenotypic states. Selection fostered inception of a developmental switch that underpinned the emergence of collectives whose fitness, during the course of evolution, became decoupled from the fitness of constituent cells. Such development and decoupling did not occur when groups reproduced via a cheat-purging regime. Our findings capture key events in the evolution of Darwinian individuality during the transition from single cells to multicellularity.

Selection methods regulate evolution of cooperation in digital evolution

PubMed Central

Lichocki, Paweł; Floreano, Dario; Keller, Laurent

2014-01-01

A key, yet often neglected, component of digital evolution and evolutionary models is the ‘selection method’ which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with formal analysis and numerical experiments the evolution of cooperation under the five most common selection methods (proportionate, rank, truncation-proportionate, truncation-uniform and tournament). We consider related individuals engaging in a Prisoner's Dilemma game where individuals can either cooperate or defect. A cooperator pays a cost, whereas its partner receives a benefit, which affect their performance scores. These performance scores are translated into fitness by one of the five selection methods. We show that cooperation is positively associated with the relatedness between individuals under all selection methods. By contrast, the change in the performance benefit of cooperation affects the populations’ average level of cooperation only under the proportionate methods. We also demonstrate that the truncation and tournament methods may introduce negative frequency-dependence and lead to the evolution of polymorphic populations. Using the example of the evolution of cooperation, we show that the choice of selection method, though it is often marginalized, can considerably affect the evolutionary dynamics. PMID:24152811

Evolution: like any other science it is predictable

PubMed Central

Conway Morris, Simon

2010-01-01

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology (‘evolution explains evolution’). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein. PMID:20008391

Sexual selection expedites the evolution of pesticide resistance.

PubMed

Jacomb, Frances; Marsh, Jason; Holman, Luke

2016-12-01

The evolution of insecticide resistance by crop pests and disease vectors causes serious problems for agriculture and health. Sexual selection can accelerate or hinder adaptation to abiotic challenges in a variety of ways, but the effect of sexual selection on resistance evolution is little studied. Here, we examine this question using experimental evolution in the pest insect Tribolium castaneum. The experimental removal of sexual selection slowed the evolution of resistance in populations treated with pyrethroid pesticide, and also reduced the rate at which resistance was lost from pesticide-free populations. These results suggest that selection arising from variance in mating and fertilization success can augment natural selection on pesticide resistance, meaning that sexual selection should be considered when designing strategies to limit the evolution of pesticide resistance. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

PubMed Central

2012-01-01

Abstract Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the “mutational landscape” model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Reviewers Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article. PMID:23062217

The modern theory of biological evolution: an expanded synthesis.

PubMed

Kutschera, Ulrich; Niklas, Karl J

2004-06-01

In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwin's Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwin's perspective. Weismann's neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwin's dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the "modern synthesis" is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.

The modern theory of biological evolution: an expanded synthesis

NASA Astrophysics Data System (ADS)

Kutschera, Ulrich; Niklas, Karl J.

In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwin's Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwin's perspective. Weismann's neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwin's dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the ``modern synthesis'' is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.

Cultural transmission and the evolution of human behaviour: a general approach based on the Price equation.

PubMed

El Mouden, C; André, J-B; Morin, O; Nettle, D

2014-02-01

Transmitted culture can be viewed as an inheritance system somewhat independent of genes that is subject to processes of descent with modification in its own right. Although many authors have conceptualized cultural change as a Darwinian process, there is no generally agreed formal framework for defining key concepts such as natural selection, fitness, relatedness and altruism for the cultural case. Here, we present and explore such a framework using the Price equation. Assuming an isolated, independently measurable culturally transmitted trait, we show that cultural natural selection maximizes cultural fitness, a distinct quantity from genetic fitness, and also that cultural relatedness and cultural altruism are not reducible to or necessarily related to their genetic counterparts. We show that antagonistic coevolution will occur between genes and culture whenever cultural fitness is not perfectly aligned with genetic fitness, as genetic selection will shape psychological mechanisms to avoid susceptibility to cultural traits that bear a genetic fitness cost. We discuss the difficulties with conceptualizing cultural change using the framework of evolutionary theory, the degree to which cultural evolution is autonomous from genetic evolution, and the extent to which cultural change should be seen as a Darwinian process. We argue that the nonselection components of evolutionary change are much more important for culture than for genes, and that this and other important differences from the genetic case mean that different approaches and emphases are needed for cultural than genetic processes. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Repeated evolution of camouflage in speciose desert rodents.

PubMed

Boratyński, Zbyszek; Brito, José C; Campos, João C; Cunha, José L; Granjon, Laurent; Mappes, Tapio; Ndiaye, Arame; Rzebik-Kowalska, Barbara; Serén, Nina

2017-06-14

There are two main factors explaining variation among species and the evolution of characters along phylogeny: adaptive change, including phenotypic and genetic responses to selective pressures, and phylogenetic inertia, or the resemblance between species due to shared phylogenetic history. Phenotype-habitat colour match, a classic Darwinian example of the evolution of camouflage (crypsis), offers the opportunity to test the importance of historical versus ecological mechanisms in shaping phenotypes among phylogenetically closely related taxa. To assess it, we investigated fur (phenotypic data) and habitat (remote sensing data) colourations, along with phylogenetic information, in the species-rich Gerbillus genus. Overall, we found a strong phenotype-habitat match, once the phylogenetic signal is taken into account. We found that camouflage has been acquired and lost repeatedly in the course of the evolutionary history of Gerbillus. Our results suggest that fur colouration and its covariation with habitat is a relatively labile character in mammals, potentially responding quickly to selection. Relatively unconstrained and substantial genetic basis, as well as structural and functional independence from other fitness traits of mammalian colouration might be responsible for that observation.

Natural selection in chemical evolution.

PubMed

Fernando, Chrisantha; Rowe, Jonathan

2007-07-07

We propose that chemical evolution can take place by natural selection if a geophysical process is capable of heterotrophic formation of liposomes that grow at some base rate, divide by external agitation, and are subject to stochastic chemical avalanches, in the absence of nucleotides or any monomers capable of modular heredity. We model this process using a simple hill-climbing algorithm, and an artificial chemistry that is unique in exhibiting conservation of mass and energy in an open thermodynamic system. Selection at the liposome level results in the stabilization of rarely occurring molecular autocatalysts that either catalyse or are consumed in reactions that confer liposome level fitness; typically they contribute in parallel to an increasingly conserved intermediary metabolism. Loss of competing autocatalysts can sometimes be adaptive. Steady-state energy flux by the individual increases due to the energetic demands of growth, but also of memory, i.e. maintaining variations in the chemical network. Self-organizing principles such as those proposed by Kauffman, Fontana, and Morowitz have been hypothesized as an ordering principle in chemical evolution, rather than chemical evolution by natural selection. We reject those notions as either logically flawed or at best insufficient in the absence of natural selection. Finally, a finite population model without elitism shows the practical evolutionary constraints for achieving chemical evolution by natural selection in the lab.

Directed evolution of cell size in Escherichia coli.

PubMed

Yoshida, Mari; Tsuru, Saburo; Hirata, Naoko; Seno, Shigeto; Matsuda, Hideo; Ying, Bei-Wen; Yomo, Tetsuya

2014-12-17

In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies.

Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

PubMed Central

Garvin, Michael R.; Bielawski, Joseph P.; Gharrett, Anthony J.

2011-01-01

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm. PMID:21969854

Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon.

PubMed

Garvin, Michael R; Bielawski, Joseph P; Gharrett, Anthony J

2011-01-01

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm.

Hierarchy and extremes in selections from pools of randomized proteins

PubMed Central

Boyer, Sébastien; Biswas, Dipanwita; Kumar Soshee, Ananda; Scaramozzino, Natale; Nizak, Clément; Rivoire, Olivier

2016-01-01

Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different “frameworks” typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution). PMID:26969726

Hierarchy and extremes in selections from pools of randomized proteins.

PubMed

Boyer, Sébastien; Biswas, Dipanwita; Kumar Soshee, Ananda; Scaramozzino, Natale; Nizak, Clément; Rivoire, Olivier

2016-03-29

Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different "frameworks" typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution).

The Theory of Evolution: An Educational Perspective.

ERIC Educational Resources Information Center

Johnson, William L.; Johnson, Annabel M.

The article's thesis is that evolution's intellectual foundations have been steadily eroding, and that few new findings in embryology, taxonomy, fossil remains, and molecular biology are bringing us very near to a formal, logical disproof of Darwinian claims. The paper begins by discussing the evidence of a prehistoric world, then they discuss…

Genome-wide scans for loci under selection in humans

PubMed Central

2005-01-01

Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA sequencing and single nucleotide polymorphism genotyping have enabled several genome-wide scans of natural selection to be undertaken. Here, some of the observations that are beginning to emerge from these studies will be reviewed, including evidence for geographically restricted selective pressures (ie local adaptation) and a relationship between genes subject to natural selection and human disease. In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection. PMID:16004726

Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA.

PubMed

Saladino, Raffaele; Šponer, Judit E; Šponer, Jiří; Costanzo, Giovanna; Pino, Samanta; Di Mauro, Ernesto

2018-06-20

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.

A role for relaxed selection in the evolution of the language capacity

PubMed Central

Deacon, Terrence W.

2010-01-01

Explaining the extravagant complexity of the human language and our competence to acquire it has long posed challenges for natural selection theory. To answer his critics, Darwin turned to sexual selection to account for the extreme development of language. Many contemporary evolutionary theorists have invoked incredibly lucky mutation or some variant of the assimilation of acquired behaviors to innate predispositions in an effort to explain it. Recent evodevo approaches have identified developmental processes that help to explain how complex functional synergies can evolve by Darwinian means. Interestingly, many of these developmental mechanisms bear a resemblance to aspects of Darwin's mechanism of natural selection, often differing only in one respect (e.g., form of duplication, kind of variation, competition/cooperation). A common feature is an interplay between processes of stabilizing selection and processes of relaxed selection at different levels of organism function. These may play important roles in the many levels of evolutionary process contributing to language. Surprisingly, the relaxation of selection at the organism level may have been a source of many complex synergistic features of the human language capacity, and may help explain why so much language information is “inherited” socially. PMID:20445088

Sexual selection and genital evolution: an overview.

PubMed

Shamloul, Rany; el-Sakka, Ahmed; Bella, Anthony J

2010-05-01

Genital morphology (especially male) among the animal kingdom is characterized by extensive differences that even members of closely related species with similar general morphology may have remarkably diverse genitalia. To present the sexual medicine specialist with a basic understanding of the current hypotheses on genital evolution with an emphasis on the sexual selection theories. A review of current literature on the theories of genital evolution. Analysis of the supporting evidence for the sexual selection theories of genital evolution. Several theories have been proposed to explain genital evolution. Currently, the sexual selection theories are being considered to present valid and solid evidence explaining genital evolution. However, other theories, including sexual conflict, are still being investigated. All theories of genital evolution have their own weaknesses and strengths. Given that many complex biological mechanisms, mostly unknown yet, are involved in the process of genital evolution, it is thus reasonable to conclude that not one theory can independently explain genital evolution. It is likely that these mechanisms may prove to have synergistic rather than exclusive effects.

Darwinism and the Behavioral Theory of Sociocultural Evolution: An Analysis.

ERIC Educational Resources Information Center

Langdon, John

1979-01-01

Challenges the view that the social sciences are theoretically impoverished disciplines when compared with the natural sciences. Demonstrates that the synthesis of an abstract Darwinian model of systemic adaptation and the behavioral principles of social learning produces a logical theory of sociocultural evolution. (DB)

Gene–culture interaction and the evolution of the human sense of fairness

PubMed Central

Liu, Tru-Gin; Lu, Yao

2016-01-01

How Darwinian evolution would produce creatures with the proclivity of Darwinian generosity, most of them voluntarily giving up the immediate benefit for themselves or their genes, remains a puzzle. This study targets a problem, the origin of human sense of fairness, and uses fairness-related genes and the social manipulation of Darwinian generosity as the key variables underlying the human sense of fairness, inequity aversion, as well as their relationships within cooperation, and the anticipation foresight of the way relationships are affected by resource division, given the assumption of randomly matched partners. Here we suggest a model in which phenotype will gradually converge towards the perfect sense of fairness along with the prospect of cooperation. Later, the sense of fairness will decrease but it is never extinct. Where social manipulation of Darwinian generosity overshadows genetics, the sense of fairness could be acute to the degree of social manipulation. Above all, there still exists a threshold in the degree of social manipulation, beyond which altruism dominates selfishness in human cooperation. Finally, we propose three new directions toward more realistic scenarios stimulated by recent development of the synergy between statistical physics, network science and evolutionary game theory. PMID:27562008

Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection

PubMed Central

Zhang, Jianzhi; Dyer, Kimberly D.; Rosenberg, Helene F.

2000-01-01

The mammalian RNase A superfamily comprises a diverse array of ribonucleolytic proteins that have a variety of biochemical activities and physiological functions. Two rapidly evolving RNases of higher primates are of particular interest as they are major secretory proteins of eosinophilic leukocytes and have been found to possess anti-pathogen activities in vitro. To understand how these RNases acquired this function during evolution and to develop animal models for the study of their functions in vivo, it is necessary to investigate these genes in many species. Here, we report the sequences of 38 functional genes and 23 pseudogenes of the eosinophil-associated RNase (EAR) family from 5 rodent species. Our phylogenetic analysis of these genes showed a clear pattern of evolution by a rapid birth-and-death process and gene sorting, a process characterized by rapid gene duplication and deactivation occurring differentially among lineages. This process ultimately generates distinct or only partially overlapping inventories of the genes, even in closely related species. Positive Darwinian selection also contributed to the diversification of these EAR genes. The striking similarity between the evolutionary patterns of the EAR genes and those of the major histocompatibility complex, immunoglobulin, and T cell receptor genes stands in strong support of the hypothesis that host-defense and generation of diversity are among the primary physiological function of the rodent EARs. The discovery of a large number of divergent EARs suggests the intriguing possibility that these proteins have been specifically tailored to fight against distinct rodent pathogens. PMID:10758160

Clonal evolution in hematologic malignancies and therapeutic implications

PubMed Central

Landau, Dan A.; Carter, Scott L.; Getz, Gad; Wu, Catherine J.

2014-01-01

The ability of cancer to evolve and adapt is a principal challenge to therapy in general, and to the paradigm of targeted therapy in particular. This ability is fueled by the co-existence of multiple, genetically heterogeneous subpopulations within the cancer cell population. Increasing evidence has supported the idea that these subpopulations are selected in a Darwinian fashion, by which the genetic landscape of the tumor is continuously reshaped. Massively parallel sequencing has enabled a recent surge in our ability to study this process, adding to previous efforts using cytogenetic methods and targeted sequencing. Altogether, these studies reveal the complex evolutionary trajectories occurring across individual hematological malignancies. They also suggest that while clonal evolution may contribute to resistance to therapy, treatment may also hasten the evolutionary process. New insights into this process challenge us to understand the impact of treatment on clonal evolution, and inspire the development of novel prognostic and therapeutic strategies. PMID:23979521

An evolutionary perspective on the systems of adaptive immunity.

PubMed

Müller, Viktor; de Boer, Rob J; Bonhoeffer, Sebastian; Szathmáry, Eörs

2018-02-01

We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of

Science for Survival: The Modern Synthesis of Evolution and the Biological Sciences Curriculum Study

ERIC Educational Resources Information Center

Green, Lisa Anne

2012-01-01

In this historical dissertation, I examined the process of curriculum development in the Biological Sciences Curriculum Study (BSCS) in the United States during the period 1959-1963. The presentation of evolution in the high school texts was based on a more robust form of Darwinian evolution which developed during the 1930s and 1940s called…

A general theory of evolution based on energy efficiency: its implications for diseases.

PubMed

Yun, Anthony J; Lee, Patrick Y; Doux, John D; Conley, Buford R

2006-01-01

We propose a general theory of evolution based on energy efficiency. Life represents an emergent property of energy. The earth receives energy from cosmic sources such as the sun. Biologic life can be characterized by the conversion of available energy into complex systems. Direct energy converters such as photosynthetic microorganisms and plants transform light energy into high-energy phosphate bonds that fuel biochemical work. Indirect converters such as herbivores and carnivores predominantly feed off the food chain supplied by these direct converters. Improving energy efficiency confers competitive advantage in the contest among organisms for energy. We introduce a term, return on energy (ROE), as a measure of energy efficiency. We define ROE as a ratio of the amount of energy acquired by a system to the amount of energy consumed to generate that gain. Life-death cycling represents a tactic to sample the environment for innovations that allow increases in ROE to develop over generations rather than an individual lifespan. However, the variation-selection strategem of Darwinian evolution may define a particular tactic rather than an overarching biological paradigm. A theory of evolution based on competition for energy and driven by improvements in ROE both encompasses prior notions of evolution and portends post-Darwinian mechanisms. Such processes may involve the exchange of non-genetic traits that improve ROE, as exemplified by cognitive adaptations or memes. Under these circumstances, indefinite persistence may become favored over life-death cycling, as increases in ROE may then occur more efficiently within a single lifespan rather than over multiple generations. The key to this transition may involve novel methods to address the promotion of health and cognitive plasticity. We describe the implications of this theory for human diseases.

Cui bono? A review of breaking the spell: religion as a natural phenomenon by Daniel C. Dennett.

PubMed

Rachlin, Howard

2007-01-01

The three requirements for a Darwinian evolutionary process are replication, variation and selection. Dennett (2006) discusses various theories of how these three processes, especially selection, may have operated in the evolution of religion. He believes that the origins of religion, like the origins of language and music, may be approached scientifically. He hopes that such investigations will open a dialog between science and religion leading to moderation of current religious extremism. One problem with Dennett's program, illustrating the difficulty of breaking away from creationist thinking, is Dennett's own failure to consider how Darwinian methods may be used to study evolution of behavioral patterns over the lifetime of individual organisms.

Dynamics of Tumor Heterogeneity Derived from Clonal Karyotypic Evolution.

PubMed

Laughney, Ashley M; Elizalde, Sergi; Genovese, Giulio; Bakhoum, Samuel F

2015-08-04

Numerical chromosomal instability is a ubiquitous feature of human neoplasms. Due to experimental limitations, fundamental characteristics of karyotypic changes in cancer are poorly understood. Using an experimentally inspired stochastic model, based on the potency and chromosomal distribution of oncogenes and tumor suppressor genes, we show that cancer cells have evolved to exist within a narrow range of chromosome missegregation rates that optimizes phenotypic heterogeneity and clonal survival. Departure from this range reduces clonal fitness and limits subclonal diversity. Mapping of the aneuploid fitness landscape reveals a highly favorable, commonly observed, near-triploid state onto which evolving diploid- and tetraploid-derived populations spontaneously converge, albeit at a much lower fitness cost for the latter. Finally, by analyzing 1,368 chromosomal translocation events in five human cancers, we find that karyotypic evolution also shapes chromosomal translocation patterns by selecting for more oncogenic derivative chromosomes. Thus, chromosomal instability can generate the heterogeneity required for Darwinian tumor evolution. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Getting Past the RNA World: The Initial Darwinian Ancestor

PubMed Central

Yarus, Michael

2011-01-01

SUMMARY A little-noted result of the confirmation of multiple premises of the RNA-world hypothesis is that we now know something about the dawn organisms that followed the origin of life, perhaps over 4 billion years ago. We are therefore in an improved position to reason about the biota just before RNA times, during the era of the first replicators, the first Darwinian creatures on Earth. An RNA congener still prominent in modern biology is a plausible descendent of these first replicators. PMID:20719875

Darwin's forgotten idea: the social essence of sexual selection.

PubMed

West-Eberhard, Mary Jane

2014-10-01

Darwinian sexual selection can now be seen in the broader context of social selection, or social competition for resources (under sexual selection, mates or fertilization success). The social-interaction aspects of sexually selected traits give them special evolutionary properties of interest for neurobiological studies of stimulus-response systems because they can account for highly complex systems with little information content other than stimulatory effectiveness per se. But these special properties have a long history of being forgotten when other factors dominate the analysis of male-female interactions, such as the mistaken belief that differential responsiveness to signals produced by competing rivals ("female choice") requires an esthetic sense; that species recognition explains all species-specific sexual signals; and, more recently, that successful signals must reflect good survival genes; or that male-female conflict involves female resistance rather than stimulus evaluation. A "conflict paradox" results when male-female conflict is seen as driven by natural selection, whose costs should often move the hypothesized "sexually antagonistic co-evolution" of sensory-response systems toward the powerful domain of sexually synergistic co-evolution under sexual selection. Special properties of sexual selection apply to other forms of social competition as well, showing the wisdom of Darwin's setting it apart from natural selection as an explanation of many otherwise puzzling and extreme traits. Copyright © 2014. Published by Elsevier Ltd.

Accelerated Evolution of the Pituitary Adenylate Cyclase-Activating Polypeptide Precursor Gene During Human Origin

PubMed Central

Wang, Yin-qiu; Qian, Ya-ping; Yang, Su; Shi, Hong; Liao, Cheng-hong; Zheng, Hong-Kun; Wang, Jun; Lin, Alice A.; Cavalli-Sforza, L. Luca; Underhill, Peter A.; Chakraborty, Ranajit; Jin, Li; Su, Bing

2005-01-01

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide abundantly expressed in the central nervous system and involved in regulating neurogenesis and neuronal signal transduction. The amino acid sequence of PACAP is extremely conserved across vertebrate species, indicating a strong functional constraint during the course of evolution. However, through comparative sequence analysis, we demonstrated that the PACAP precursor gene underwent an accelerated evolution in the human lineage since the divergence from chimpanzees, and the amino acid substitution rate in humans is at least seven times faster than that in other mammal species resulting from strong Darwinian positive selection. Eleven human-specific amino acid changes were identified in the PACAP precursors, which are conserved from murine to African apes. Protein structural analysis suggested that a putative novel neuropeptide might have originated during human evolution and functioned in the human brain. Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may have contributed to the formation of human cognition. PMID:15834139

Evolution of catalytic function

NASA Technical Reports Server (NTRS)

Joyce, G. F.

1993-01-01

An RNA-based evolution system was constructed in the laboratory and used to develop RNA enzymes with novel catalytic function. By controlling the nature of the catalytic task that the molecules must perform in order to survive, it is possible to direct the evolving population toward the expression of some desired catalytic behavior. More recently, this system has been coupled to an in vitro translation procedure, raising the possibility of evolving protein enzymes in the laboratory to produce novel proteins with desired catalytic properties. The aim of this line of research is to reduce darwinian evolution, the fundamental process of biology, to a laboratory procedure that can be made to operate in the service of organic synthesis.

Estimating fisheries-induced selection: traditional gear selectivity research meets fisheries-induced evolution.

PubMed

Kuparinen, Anna; Kuikka, Sakari; Merilä, Juha

2009-05-01

The study of fisheries-induced evolution is a research field which is becoming recognized both as an important and interesting problem in applied evolution, as well as a practical management problem in fisheries. Much of the research in fisheries-induced evolution has focussed on quantifying and proving that an evolutionary response has taken place, but less effort has been invested on the actual processes and traits underlying capture of a fish by a fishing gear. This knowledge is not only needed to understand possible phenotypic selection associated to fishing but also to help to device sustainable fisheries and management strategies. Here, we draw attention to the existing knowledge about selectivity of fishing gears and outline the ways in which this information could be utilized in the context of fisheries-induced evolution. To these ends, we will introduce a mathematical framework commonly applied to quantify fishing gear selectivity, illustrate the link between gear selectivity and the change in the distribution of phenotypes induced by fishing, review what is known about selectivity of commonly used fishing gears, and discuss how this knowledge could be applied to improve attempts to predict evolutionary impacts of fishing.

Evolution of haploid selection in predominantly diploid organisms

PubMed Central

Otto, Sarah P.; Scott, Michael F.; Immler, Simone

2015-01-01

Diploid organisms manipulate the extent to which their haploid gametes experience selection. Animals typically produce sperm with a diploid complement of most proteins and RNA, limiting selection on the haploid genotype. Plants, however, exhibit extensive expression in pollen, with actively transcribed haploid genomes. Here we analyze models that track the evolution of genes that modify the strength of haploid selection to predict when evolution intensifies and when it dampens the “selective arena” within which male gametes compete for fertilization. Considering deleterious mutations, evolution leads diploid mothers to strengthen selection among haploid sperm/pollen, because this reduces the mutation load inherited by their diploid offspring. If, however, selection acts in opposite directions in haploids and diploids (“ploidally antagonistic selection”), mothers evolve to reduce haploid selection to avoid selectively amplifying alleles harmful to their offspring. Consequently, with maternal control, selection in the haploid phase either is maximized or reaches an intermediate state, depending on the deleterious mutation rate relative to the extent of ploidally antagonistic selection. By contrast, evolution generally leads diploid fathers to mask mutations in their gametes to the maximum extent possible, whenever masking (e.g., through transcript sharing) increases the average fitness of a father’s gametes. We discuss the implications of this maternal–paternal conflict over the extent of haploid selection and describe empirical studies needed to refine our understanding of haploid selection among seemingly diploid organisms. PMID:26669442

Reasons Given by UK Churchgoers for Their Stance on Evolution

ERIC Educational Resources Information Center

Village, Andrew; Baker, Sylvia

2013-01-01

A sample of 661 churchgoers from a range of Christian denominations in the United Kingdom was asked about Darwinian evolution (defined as the common origin of all species, including humans). Respondents were categorised as those who accepted the idea, those who rejected it, and those who were unsure or neutral. People in each category were given a…

Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.

PubMed

Miller, William B; Torday, John S

2018-04-13

Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory.

PubMed

Shanahan, Timothy

2008-03-01

In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.

On the thermodynamics of multilevel evolution.

PubMed

Tessera, Marc; Hoelzer, Guy A

2013-09-01

Biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term "evolution" employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Iconoclasts of Evolution: Haeckel, Behe, Wells & the Ontogeny of a Fraud

ERIC Educational Resources Information Center

Pickett, Kurt M.; Wenzel, John W.; Rissing, Steven W.

2005-01-01

Behe (1998) and Wells (1999) claimed that embryological support for Darwinian evolution is based on the drawings of the 19th century embryologist Ernst Haeckel (1834-1919) whose embryological drawings were regarded inaccurate and fraudulent. The history of modern embryology, the roles played by Von Baer and Haeckel in that history and the manner…

Sex differences, sexual selection, and ageing: an experimental evolution approach.

PubMed

Maklakov, Alexei A; Bonduriansky, Russell; Brooks, Robert C

2009-10-01

Life-history (LH) theory predicts that selection will optimize the trade-off between reproduction and somatic maintenance. Reproductive ageing and finite life span are direct consequences of such optimization. Sexual selection and conflict profoundly affect the reproductive strategies of the sexes and thus can play an important role in the evolution of life span and ageing. In theory, sexual selection can favor the evolution of either faster or slower ageing, but the evidence is equivocal. We used a novel selection experiment to investigate the potential of sexual selection to influence the adaptive evolution of age-specific LH traits. We selected replicate populations of the seed beetle Callosobruchus maculatus for age at reproduction ("Young" and "Old") either with or without sexual selection. We found that LH selection resulted in the evolution of age-specific reproduction and mortality but these changes were largely unaffected by sexual selection. Sexual selection depressed net reproductive performance and failed to promote adaptation. Nonetheless, the evolution of several traits differed between males and females. These data challenge the importance of current sexual selection in promoting rapid adaptation to environmental change but support the hypothesis that sex differences in LH-a historical signature of sexual selection-are key in shaping trait responses to novel selection.

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

PubMed

Osada, Naoki; Akashi, Hiroshi

2012-01-01

Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.

Cell-selfish modes of evolution and mutations directed after transcriptional bypass.

PubMed

Holmquist, Gerald P

2002-12-29

During transcription, prokaryotic and eukaryotic RNA polymerases bypass and misread (transcriptional mutagenesis) several classes of DNA lesions. For example, misreading of 8-OH-dG generates mRNAs containing G to T transversions. After translation, if the mutant protein briefly allowed the cell a growth-DNA replication advantage, then precocious DNA replication would bypass that unrepaired 8-OH-dG and misinsert dA opposite the directing DNA lesion with a higher probability than would be experienced for 8-OH-G lesions at other positions in otherwise identical neighboring cells. Such retromutations would have been tested for their imparted growth advantage as mRNA before they became heritable DNA mutations. The logical properties of a mode of evolution that utilizes directed-retromutagenesis were compared one by one with those of the standard neo-Darwinian mode. The retromutagenesis mode, while minimizing mutational load, is cell-selfish; fitness is for an immediate growth advantage rather than future reproductive potential. In prokaryotes, an evolutionary mode that involves standard Darwinian fitness testing of novel alleles in the genetic background of origin followed by clonal expansion also favors cell-selfish allele combinations when linkage disequilibrium is practiced. For metazoa and plants to have evolved organized tissues, cell-selfish modes of evolution represent systems-poisons that must be totally suppressed. The feedback loops that allow evolution to be cell-serving in prokaryotes are actively blocked in eukaryotes by traits that restrict fitness to future reproductive potential. These traits include (i) delay of fitness testing until after the mutation is made permanently heritable, (ii) diploidy to further delay fitness testing, (iii) segregation of somatic lines from germ lines, (iv) testing of novel alleles against randomized allele combinations constructed by obligate sex, and (v) obligate genetic death to insure that that the most basic systems

Exaptation in human evolution: how to test adaptive vs exaptive evolutionary hypotheses.

PubMed

Pievani, Telmo; Serrelli, Emanuele

2011-01-01

Palaeontologists, Stephen J. Gould and Elisabeth Vrba, introduced the term "ex-aptation" with the aim of improving and enlarging the scientific language available to researchers studying the evolution of any useful character, instead of calling it an "adaptation" by default, coming up with what Gould named an "extended taxonomy of fitness". With the extension to functional co-optations from non-adaptive structures ("spandrels"), the notion of exaptation expanded and revised the neo-Darwinian concept of "pre-adaptation" (which was misleading, for Gould and Vrba, suggesting foreordination). Exaptation is neither a "saltationist" nor an "anti-Darwinian" concept and, since 1982, has been adopted by many researchers in evolutionary and molecular biology, and particularly in human evolution. Exaptation has also been contested. Objections include the "non-operationality objection".We analyze the possible operationalization of this concept in two recent studies, and identify six directions of empirical research, which are necessary to test "adaptive vs. exaptive" evolutionary hypotheses. We then comment on a comprehensive survey of literature (available online), and on the basis of this we make a quantitative and qualitative evaluation of the adoption of the term among scientists who study human evolution. We discuss the epistemic conditions that may have influenced the adoption and appropriate use of exaptation, and comment on the benefits of an "extended taxonomy of fitness" in present and future studies concerning human evolution.

A Computational Model of Selection by Consequences

ERIC Educational Resources Information Center

McDowell, J. J.

2004-01-01

Darwinian selection by consequences was instantiated in a computational model that consisted of a repertoire of behaviors undergoing selection, reproduction, and mutation over many generations. The model in effect created a digital organism that emitted behavior continuously. The behavior of this digital organism was studied in three series of…

Three Decades of Anti-evolution Campaign and its Results: Turkish Undergraduates' Acceptance and Understanding of the Biological Evolution Theory

NASA Astrophysics Data System (ADS)

Peker, Deniz; Comert, Gulsum Gul; Kence, Aykut

2010-06-01

Even though in the early years of the Republic of Turkey Darwin’s theory of evolution was treated as a scientific theory and taught fairly in schools, despite all the substantial evidence accumulated supporting the theory of evolution since then, Darwin and his ideas today have been scorned by curriculum and education policy makers. Furthermore, Turkish students and academics have been faced with unprecedented creationist propaganda for many years. In this paper, we first provide a glimpse of the theory of evolution and creationism in Turkey, we then report the results of our survey study ( N = 1,098) about the undergraduates’ acceptance and understanding of Darwinian evolution and some of the socioeconomic variables affecting those measures. Our cross sectional study shows that acceptance and understanding of the theory of evolution is quite low. We criticize the current state of evolution education in Turkey and call for a change towards a scientific treatment of the theory evolution in schools.

Re-Evaluating Clonal Dominance in Cancer Evolution.

PubMed

Burrell, Rebecca A; Swanton, Charles

2016-05-01

Tumours are composed of genetically heterogeneous subclones which may diverge early during tumour growth. However, our strategies for treating and assessing outcome for patients are overwhelmingly based upon the classical linear paradigm for cancer evolution. Increasing numbers of studies are finding that minor subclones can determine clinical disease course, and that temporal and spatial heterogeneity needs to be considered in disease management. In this article we review evidence for cancer clonal heterogeneity, evaluating the importance of tumour subclones and their growth through both Darwinian and neutral evolution. Major shifts in current clinical practice and trial designs, aimed at understanding cancer evolution on a patient-by-patient basis, may be necessary to achieve more successful treatment of heterogeneous metastatic disease. Copyright © 2016 Elsevier Inc. All rights reserved.

Phenotypic plasticity, the Baldwin effect, and the speeding up of evolution: the computational roots of an illusion.

PubMed

Santos, Mauro; Szathmáry, Eörs; Fontanari, José F

2015-04-21

An increasing number of dissident voices claim that the standard neo-Darwinian view of genes as 'leaders' and phenotypes as 'followers' during the process of adaptive evolution should be turned on its head. This idea is older than the rediscovery of Mendel's laws of inheritance, with the turn-of-the-twentieth-century notion eventually labeled as the 'Baldwin effect' as one of the many ways in which the standard neo-Darwinian view can be turned around. A condition for this effect is that environmentally induced variation such as phenotypic plasticity or learning is crucial for the initial establishment of a trait. This gives the additional time for natural selection to act on genetic variation and the adaptive trait can be eventually encoded in the genotype. An influential paper published in the late 1980s claimed the Baldwin effect to happen in computer simulations, and avowed that it was crucial to solve a difficult adaptive task. This generated much excitement among scholars in various disciplines that regard neo-Darwinian accounts to explain the evolutionary emergence of high-order phenotypic traits such as consciousness or language almost hopeless. Here, we use analytical and computational approaches to show that a standard population genetics treatment can easily crack what the scientific community has granted as an unsolvable adaptive problem without learning. Evolutionary psychologists and linguists have invoked the (claimed) Baldwin effect to make wild assertions that should not be taken seriously. What the Baldwin effect needs are plausible case-histories. Copyright © 2015 Elsevier Ltd. All rights reserved.

Selection within organisms in the nineteenth century: Wilhelm Roux's complex legacy.

PubMed

Heams, Thomas

2012-09-01

Selectionism, or the extension of darwinian chance/selection dynamics beyond the individual level, has a long history in biological thought. It has generated important theories in immunology or neurology, and turns out to be a convincing framework to account for the intrinsic stochastic nature of core events in cellular biology. When looking back at the intellectual origins of selectionism, the essay by the German embryologist Wilhelm Roux, Der Kampf der Theile im Organismus (The Struggle of the Parts in the Organism - 1881) might be one, if not the earliest reference after the darwinian revolution. It describes the individual as a multilevel structure, where each level results from a 'darwinian' struggle of its parts (molecules, cells, tissues, organs). But Roux's theory, far from being a simple extension of natural selection, has complex and even conflictual relationships with darwinism. This essay is worth rediscovering as a subtle historical testimony of the evolutionary and developmental life sciences debates of its time. Moreover, some of its theses may also enrich some current debates among evolutionary biologists over levels of selection, and among cellular and molecular biologists over the status of determinism in biology today. Copyright © 2012 Elsevier Ltd. All rights reserved.

CLONAL EVOLUTION IN CANCER

PubMed Central

Greaves, Mel; Maley, Carlo C.

2012-01-01

Cancers evolve by a reiterative process of clonal expansion, genetic diversification and clonal selection within the adaptive landscapes of tissue ecosystems. The dynamics are complex with highly variable patterns of genetic diversity and resultant clonal architecture. Therapeutic intervention may decimate cancer clones, and erode their habitats, but inadvertently provides potent selective pressure for the expansion of resistant variants. The inherently Darwinian character of cancer lies at the heart of therapeutic failure but perhaps also holds the key to more effective control. PMID:22258609

Evolution: bats, radar, and science (The Remote Sensing Award Lecture)

NASA Technical Reports Server (NTRS)

Atlas, David

1991-01-01

A parallel is drawn between the evolution of the bat and the evolution of the science and technology of radar and remote sensing to illustrate the importance of the role of Darwinian processes in the culture and practice of science and technology, and thus in the survival of their vitality. The lecture touches on several themes of interest to the science community, such as the relation between basic and applied science and engineering; research in academia, industry, and government laboratories; elite scientists; and the survival of a scientific institution.

Selection, constraint, and the evolution of coloration in African starlings.

PubMed

Maia, Rafael; Rubenstein, Dustin R; Shawkey, Matthew D

2016-05-01

Colorful plumage plays a prominent role in the evolution of birds, influencing communication (sexual/social selection), and crypsis (natural selection). Comparative studies have focused primarily on these selective pressures, but the mechanisms underlying color production can also be important by constraining the color gamut upon which selection acts. Iridescence is particularly interesting to study the interaction between selection and color-producing mechanisms because a broad range of colors can be produced with a shared template, and innovations to this template further expand this by increasing the parameters interacting to produce colors. We examine the patterns of ornamentation and dichromatism evolution in African starlings, a group remarkably diverse in color production mechanisms, social systems, and ecologies. We find that the presence of iridescence is ancestral to the group, being predominantly lost in females and cooperative breeders, as well as species with less labile templates. Color-producing mechanisms interact and are the main predictors of plumage ornamentation and elaboration, with little influence of selective pressures in their evolution. Dichromatism, however is influenced by social system and the loss of iridescence. Our results show the importance of considering both selection and constraints, and the different roles that they may have, in the evolution of ornamentation and dimorphism. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Discovery of a Distinct Superfamily of Kunitz-Type Toxin (KTT) from Tarantulas

PubMed Central

Diao, Jian-Bo; Jiang, Li-Ping; Tang, Xing; Liang, Song-Ping

2008-01-01

Background Kuntiz-type toxins (KTTs) have been found in the venom of animals such as snake, cone snail and sea anemone. The main ancestral function of Kunitz-type proteins was the inhibition of a diverse array of serine proteases, while toxic activities (such as ion-channel blocking) were developed under a variety of Darwinian selection pressures. How new functions were grafted onto an old protein scaffold and what effect Darwinian selection pressures had on KTT evolution remains a puzzle. Principal Findings Here we report the presence of a new superfamily of KTTs in spiders (Tarantulas: Ornithoctonus huwena and Ornithoctonus hainana), which share low sequence similarity to known KTTs and is clustered in a distinct clade in the phylogenetic tree of KTT evolution. The representative molecule of spider KTTs, HWTX-XI, purified from the venom of O. huwena, is a bi-functional protein which is a very potent trypsin inhibitor (about 30-fold more strong than BPTI) as well as a weak Kv1.1 potassium channel blocker. Structural analysis of HWTX-XI in 3-D by NMR together with comparative function analysis of 18 expressed mutants of this toxin revealed two separate sites, corresponding to these two activities, located on the two ends of the cone-shape molecule of HWTX-XI. Comparison of non-synonymous/synonymous mutation ratios (ω) for each site in spider and snake KTTs, as well as PBTI like body Kunitz proteins revealed high Darwinian selection pressure on the binding sites for Kv channels and serine proteases in snake, while only on the proteases in spider and none detected in body proteins, suggesting different rates and patterns of evolution among them. The results also revealed a series of key events in the history of spider KTT evolution, including the formation of a novel KTT family (named sub-Kuntiz-type toxins) derived from the ancestral native KTTs with the loss of the second disulfide bridge accompanied by several dramatic sequence modifications. Conclusions

A (historical) remark on the Darwin-Schiaparelli evolution theory.

PubMed

Freguglia, Paolo

2016-01-01

The aim of this paper is a free interpretation and reconstruction of a part of Giovanni Virginio Schiaparelli's essay (1898) where the author presents some ideas about a correspondence between living organisms and geometrical curves. From our analysis we derive a new approach to the ago-antagonist conception of the Darwinian evolution theory which is a continuation of [2]. Copyright: © 2016 by Fabrizio Serra editore, Pisa · Roma.

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life

PubMed Central

Koonin, Eugene V

2007-01-01

Background Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception. Hypothesis Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse). Conclusion The

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life.

PubMed

Koonin, Eugene V

2007-05-31

Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception. Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse). The plausibility of different models

Selectionist and Evolutionary Approaches to Brain Function: A Critical Appraisal

PubMed Central

Fernando, Chrisantha; Szathmáry, Eörs; Husbands, Phil

2012-01-01

We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse, and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity, and variability) as the most powerful mechanism for search in a sparsely occupied search space. Examples are given of cases where parallel competitive search with information transfer among the units is more efficient than search without information transfer between units. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise. PMID:22557963

A paradigm for viewing biologic systems as scale-free networks based on energy efficiency: implications for present therapies and the future of evolution.

PubMed

Yun, Anthony J; Lee, Patrick Y; Doux, John D

2006-01-01

A network constitutes an abstract description of the relationships among entities, respectively termed links and nodes. If a power law describes the probability distribution of the number of links per node, the network is said to be scale-free. Scale-free networks feature link clustering around certain hubs based on preferential attachments that emerge due either to merit or legacy. Biologic systems ranging from sub-atomic to ecosystems represent scale-free networks in which energy efficiency forms the basis of preferential attachments. This paradigm engenders a novel scale-free network theory of evolution based on energy efficiency. As environmental flux induces fitness dislocations and compels a new meritocracy, new merit-based hubs emerge, previously merit-based hubs become legacy hubs, and network recalibration occurs to achieve system optimization. To date, Darwinian evolution, characterized by innovation sampling, variation, and selection through filtered termination, has enabled biologic progress through optimization of energy efficiency. However, as humans remodel their environment, increasing the level of unanticipated fitness dislocations and inducing evolutionary stress, the tendency of networks to exhibit inertia and retain legacy hubs engender maladaptations. Many modern diseases may fundamentally derive from these evolutionary displacements. Death itself may constitute a programmed adaptation, terminating individuals who represent legacy hubs and recalibrating the network. As memes replace genes as the basis of innovation, death itself has become a legacy hub. Post-Darwinian evolution may favor indefinite persistence to optimize energy efficiency. We describe strategies to reprogram or decommission legacy hubs that participate in human disease and death.

"The Two Brothers": Reconciling Perceptual-Cognitive and Statistical Models of Musical Evolution.

PubMed

Jan, Steven

2018-01-01

While the "units, events and dynamics" of memetic evolution have been abstractly theorized (Lynch, 1998), they have not been applied systematically to real corpora in music. Some researchers, convinced of the validity of cultural evolution in more than the metaphorical sense adopted by much musicology, but perhaps skeptical of some or all of the claims of memetics, have attempted statistically based corpus-analysis techniques of music drawn from molecular biology, and these have offered strong evidence in favor of system-level change over time (Savage, 2017). This article argues that such statistical approaches, while illuminating, ignore the psychological realities of music-information grouping, the transmission of such groups with varying degrees of fidelity, their selection according to relative perceptual-cognitive salience, and the power of this Darwinian process to drive the systemic changes (such as the development over time of systems of tonal organization in music) that statistical methodologies measure. It asserts that a synthesis between such statistical approaches to the study of music-cultural change and the theory of memetics as applied to music (Jan, 2007), in particular the latter's perceptual-cognitive elements, would harness the strengths of each approach and deepen understanding of cultural evolution in music.

Sexual selection and the evolution of secondary sexual traits: sex comb evolution in Drosophila.

PubMed

Snook, Rhonda R; Gidaszewski, Nelly A; Chapman, Tracey; Simmons, Leigh W

2013-04-01

Sexual selection can drive rapid evolutionary change in reproductive behaviour, morphology and physiology. This often leads to the evolution of sexual dimorphism, and continued exaggerated expression of dimorphic sexual characteristics, although a variety of other alternative selection scenarios exist. Here, we examined the evolutionary significance of a rapidly evolving, sexually dimorphic trait, sex comb tooth number, in two Drosophila species. The presence of the sex comb in both D. melanogaster and D. pseudoobscura is known to be positively related to mating success, although little is yet known about the sexually selected benefits of sex comb structure. In this study, we used experimental evolution to test the idea that enhancing or eliminating sexual selection would lead to variation in sex comb tooth number. However, the results showed no effect of either enforced monogamy or elevated promiscuity on this trait. We discuss several hypotheses to explain the lack of divergence, focussing on sexually antagonistic coevolution, stabilizing selection via species recognition and nonlinear selection. We discuss how these are important, but relatively ignored, alternatives in understanding the evolution of rapidly evolving sexually dimorphic traits. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

The evolution of trade-offs under directional and correlational selection.

PubMed

Roff, Derek A; Fairbairn, Daphne J

2012-08-01

Using quantitative genetic theory, we develop predictions for the evolution of trade-offs in response to directional and correlational selection. We predict that directional selection favoring an increase in one trait in a trade-off will result in change in the intercept but not the slope of the trade-off function, with the mean value of the selected trait increasing and that of the correlated trait decreasing. Natural selection will generally favor an increase in some combination of trait values, which can be represented as directional selection on an index value. Such selection induces both directional and correlational selection on the component traits. Theory predicts that selection on an index value will also change the intercept but not the slope of the trade-off function but because of correlational selection, the direction of change in component traits may be in the same or opposite directions. We test these predictions using artificial selection on the well-established trade-off between fecundity and flight capability in the cricket, Gryllus firmus and compare the empirical results with a priori predictions made using genetic parameters from a separate half-sibling experiment. Our results support the predictions and illustrate the complexity of trade-off evolution when component traits are subject to both directional and correlational selection. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Stabilizing selection on sperm number revealed by artificial selection and experimental evolution.

PubMed

Cattelan, Silvia; Di Nisio, Andrea; Pilastro, Andrea

2018-03-01

Sperm competition is taxonomically widespread in animals and is usually associated with large sperm production, being the number of sperm in the competing pool the prime predictor of fertilization success. Despite the strong postcopulatory selection acting directionally on sperm production, its genetic variance is often very high. This can be explained by trade-offs between sperm production and traits associated with mate acquisition or survival, that may contribute to generate an overall stabilizing selection. To investigate this hypothesis, we first artificially selected male guppies (Poecilia reticulata) for high and low sperm production for three generations, while simultaneously removing sexual selection. Then, we interrupted artificial selection and restored sexual selection. Sperm production responded to divergent selection in one generation, and when we restored sexual selection, both high and low lines converged back to the mean sperm production of the original population within two generations, indicating that sperm number is subject to strong stabilizing total sexual selection (i.e., selection acting simultaneously on all traits associated with reproductive success). We discuss the possible mechanisms responsible for the maintenance of high genetic variability in sperm production despite strong selection acting on it. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Nothing in the History of Spanish "Anis" Makes Sense, Except in the Light of Evolution

ERIC Educational Resources Information Center

Delgado, Juan Antonio; Palma, Ricardo Luis

2011-01-01

We describe, discuss and illustrate a metaphoric parallel between the history of the most famous Spanish liqueur, "Anis del Mono" ("Anis" of the Monkey), and the evolution of living organisms in the light of Darwinian theory and other biological hypotheses published subsequent to Charles Darwin's "Origin of Species." Also, we report the use of a…

What Does "the RNA World" Mean to "the Origin of Life"?

PubMed

Ma, Wentao

2017-11-29

Corresponding to life's two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the "self-sustainment" we concern about life should be the self-sustainment of a relevant system that is "defined" by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution-provided that the genetic molecules can "simply" code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. In the light of those possible scenes included in this scenario, Darwinian evolution may have originated at the molecular level, realized upon a functional RNA. When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. But it was not until the appearance of the "unitary-protocell", which had all of its RNA genes linked into a chromosome, that Darwinian evolution made its full step towards the cellular level-no longer severely constrained by the low-grade evolution at the molecular level. Self-sustainment did not make sense before protocells emerged

Getting to Darwin: Obstacles to Accepting Evolution by Natural Selection

ERIC Educational Resources Information Center

Thagard, Paul; Findlay, Scott

2010-01-01

Darwin's theory of evolution by natural selection is central to modern biology, but is resisted by many people. This paper discusses the major psychological obstacles to accepting Darwin's theory. Cognitive obstacles to adopting evolution by natural selection include conceptual difficulties, methodological issues, and coherence problems that…

Bone-associated gene evolution and the origin of flight in birds.

PubMed

Machado, João Paulo; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; O'Brien, Stephen J; Antunes, Agostinho

2016-05-18

Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades of vertebrates, birds and bats. While this trait provided advantages such as in aerial foraging habits, escape from predators or long-distance travels, it also imposed great challenges, namely in the bone structure. We performed comparative genomic analyses of 89 bone-associated genes from 47 avian genomes (including 45 new), 39 mammalian, and 20 reptilian genomes, and demonstrate that birds, after correcting for multiple testing, have an almost two-fold increase in the number of bone-associated genes with evidence of positive selection (~52.8 %) compared with mammals (~30.3 %). Most of the positive-selected genes in birds are linked with bone regulation and remodeling and thirteen have been linked with functional pathways relevant to powered flight, including bone metabolism, bone fusion, muscle development and hyperglycemia levels. Genes encoding proteins involved in bone resorption, such as TPP1, had a high number of sites under Darwinian selection in birds. Patterns of positive selection observed in bird ossification genes suggest that there was a period of intense selective pressure to improve flight efficiency that was closely linked with constraints on body size.

Nonmathematical concepts of selection, evolutionary energy, and levels of evolution.

PubMed

Darlington, P J

1972-05-01

The place of mathematics in hypotheticodeductive processes and in biological research is discussed. (Natural) Selection is defined and described as differential elimination of performed sets at any level. Sets and acting sets are groups of units (themselves sets of smaller units) at any level that may or do interact. A pseudomathematical equation describes directional change (evolution) in sets at any level. Selection is the ram of evolution; it cannot generate, but can only direct, evolutionary energy. The energy of evolution is derived from molecular or chemical levels, is transmitted upwards through the increasingly complex sets of sets that form living systems, and is turned in directions determined by the sum of selective processes, at different levels, which may either supplement or oppose each other. All evolutionary processes conform to the pseudomathematical equation referred to above, use energy as described above, and have a P/OE (ratio of programming to open-endedness) that cannot be measured, but can be related to other P/OE values. Phylogeny and ontogeny are compared as processes af directional change with set selection. Stages in the evolution of multi-cellular individuals are suggested, and are essentially the same as stages in the evolution of some multi-individual insect societies. Thinking is considered as a part of ontogeny involving an irreversible, nonrepetitive process of set selection in the brain.

Evolution and History in a new "Mathematical SETI" model

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2014-01-01

In a recent paper (Maccone, 2011 [15]) and in a recent book (Maccone, 2012 [17]), this author proposed a new mathematical model capable of merging SETI and Darwinian Evolution into a single mathematical scheme. This model is based on exponentials and lognormal probability distributions, called "b-lognormals" if they start at any positive time b ("birth") larger than zero. Indeed: Darwinian evolution theory may be regarded as a part of SETI theory in that the factor fl in the Drake equation represents the fraction of planets suitable for life on which life actually arose, as it happened on Earth. In 2008 (Maccone, 2008 [9]) this author firstly provided a statistical generalization of the Drake equation where the number N of communicating ET civilizations in the Galaxy was shown to follow the lognormal probability distribution. This fact is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution if the number of factors is increased at will, i.e. it approaches infinity. Also, in Maccone (2011 [15]), it was shown that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of b-lognormal distributions constrained between the time axis and the exponential growth curve. This was a brand-new result. And one more new and far-reaching idea was to define Darwinian Evolution as a particular realization of a stochastic process called Geometric Brownian Motion (GBM) having the above exponential as its own mean value curve. The b-lognormals may be also be interpreted as the lifespan of any living being, let it be a cell, or an animal, a plant, a human, or even the historic lifetime of any civilization. In Maccone, (2012 [17, Chapters 6, 7, 8 and 11]), as well as in the present paper, we give

Selection by consequences, behavioral evolution, and the price equation.

PubMed

Baum, William M

2017-05-01

Price's equation describes evolution across time in simple mathematical terms. Although it is not a theory, but a derived identity, it is useful as an analytical tool. It affords lucid descriptions of genetic evolution, cultural evolution, and behavioral evolution (often called "selection by consequences") at different levels (e.g., individual vs. group) and at different time scales (local and extended). The importance of the Price equation for behavior analysis lies in its ability to precisely restate selection by consequences, thereby restating, or even replacing, the law of effect. Beyond this, the equation may be useful whenever one regards ontogenetic behavioral change as evolutionary change, because it describes evolutionary change in abstract, general terms. As an analytical tool, the behavioral Price equation is an excellent aid in understanding how behavior changes within organisms' lifetimes. For example, it illuminates evolution of response rate, analyses of choice in concurrent schedules, negative contingencies, and dilemmas of self-control. © 2017 Society for the Experimental Analysis of Behavior.

Bridging Emergent Attributes and Darwinian Principles in Teaching Natural Selection

ERIC Educational Resources Information Center

Xu, Dongchen; Chi, Michelene T. H.

2016-01-01

Students often have misconceptions about natural selection as they misuse a direct causal schema to explain the process. Natural selection is in fact an emergent process where random interactions lead to changes in a population. The misconceptions stem from students' lack of emergent schema for natural selection. In order to help students…

Danes commemorating Darwin: apes and evolution at the 1909 anniversary.

PubMed

Hjermitslev, Hans Henrik

2010-10-01

This article analyses the Danish 1909 celebrations of the centenary of Charles Darwin's birth on 12 February 1809. I argue that the 1909 meetings, lectures and publications devoted to Darwin and his theory of evolution by natural selection can be characterised by ambivalence: on the one hand, tribute to a great man of science who established a new view of nature and, on the other hand, scepticism towards the Darwinian mechanism of natural selection and the wider religious and political implications drawn from his theory. The article examines both professional and popular commemorative activities, focusing primarily on celebratory articles carried in widely circulated magazines and newspapers. I identify three types of interpretations of Darwin's ideas which I characterise as 'radical', 'evangelical' and 'safe' science. These different positions were closely linked to the political and cultural divisions of the periodical press. Moreover, my analysis of the popular press offers a solid basis for asserting that to most people Darwinism was associated with human evolution, primarily the relationship between man and apes, while more sophisticated discussions about the crisis of Darwinism prominent among naturalists played only a secondary role in the public arena. This article demonstrates the value of using newspapers as historical sources when looking for public images of Darwin, popular receptions of Darwinism and representations of science in general.

Evolution and mass extinctions as lognormal stochastic processes

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2014-10-01

In a series of recent papers and in a book, this author put forward a mathematical model capable of embracing the search for extra-terrestrial intelligence (SETI), Darwinian Evolution and Human History into a single, unified statistical picture, concisely called Evo-SETI. The relevant mathematical tools are: (1) Geometric Brownian motion (GBM), the stochastic process representing evolution as the stochastic increase of the number of species living on Earth over the last 3.5 billion years. This GBM is well known in the mathematics of finances (Black-Sholes models). Its main features are that its probability density function (pdf) is a lognormal pdf, and its mean value is either an increasing or, more rarely, decreasing exponential function of the time. (2) The probability distributions known as b-lognormals, i.e. lognormals starting at a certain positive instant b>0 rather than at the origin. These b-lognormals were then forced by us to have their peak value located on the exponential mean-value curve of the GBM (Peak-Locus theorem). In the framework of Darwinian Evolution, the resulting mathematical construction was shown to be what evolutionary biologists call Cladistics. (3) The (Shannon) entropy of such b-lognormals is then seen to represent the `degree of progress' reached by each living organism or by each big set of living organisms, like historic human civilizations. Having understood this fact, human history may then be cast into the language of b-lognormals that are more and more organized in time (i.e. having smaller and smaller entropy, or smaller and smaller `chaos'), and have their peaks on the increasing GBM exponential. This exponential is thus the `trend of progress' in human history. (4) All these results also match with SETI in that the statistical Drake equation (generalization of the ordinary Drake equation to encompass statistics) leads just to the lognormal distribution as the probability distribution for the number of extra

Bayesian Methods and Universal Darwinism

NASA Astrophysics Data System (ADS)

Campbell, John

2009-12-01

Bayesian methods since the time of Laplace have been understood by their practitioners as closely aligned to the scientific method. Indeed a recent Champion of Bayesian methods, E. T. Jaynes, titled his textbook on the subject Probability Theory: the Logic of Science. Many philosophers of science including Karl Popper and Donald Campbell have interpreted the evolution of Science as a Darwinian process consisting of a `copy with selective retention' algorithm abstracted from Darwin's theory of Natural Selection. Arguments are presented for an isomorphism between Bayesian Methods and Darwinian processes. Universal Darwinism, as the term has been developed by Richard Dawkins, Daniel Dennett and Susan Blackmore, is the collection of scientific theories which explain the creation and evolution of their subject matter as due to the Operation of Darwinian processes. These subject matters span the fields of atomic physics, chemistry, biology and the social sciences. The principle of Maximum Entropy states that Systems will evolve to states of highest entropy subject to the constraints of scientific law. This principle may be inverted to provide illumination as to the nature of scientific law. Our best cosmological theories suggest the universe contained much less complexity during the period shortly after the Big Bang than it does at present. The scientific subject matter of atomic physics, chemistry, biology and the social sciences has been created since that time. An explanation is proposed for the existence of this subject matter as due to the evolution of constraints in the form of adaptations imposed on Maximum Entropy. It is argued these adaptations were discovered and instantiated through the Operations of a succession of Darwinian processes.

Directed Bak-Sneppen Model for Food Chains

NASA Astrophysics Data System (ADS)

Stauffer, D.; Jan, N.

A modification of the Bak-Sneppen model to include simple elements of Darwinian evolution is used to check the survival of prey and predators in long food chains. Mutations, selection, and starvation resulting from depleted prey are incorporated in this model.

What Does “the RNA World” Mean to “the Origin of Life”?

PubMed Central

Ma, Wentao

2017-01-01

Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. In the light of those possible scenes included in this scenario, Darwinian evolution may have originated at the molecular level, realized upon a functional RNA. When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. But it was not until the appearance of the “unitary-protocell”, which had all of its RNA genes linked into a chromosome, that Darwinian evolution made its full step towards the cellular level—no longer severely constrained by the low-grade evolution at the molecular level. Self-sustainment did not make sense before

The evolution of wealth transmission in human populations: a stochastic model

NASA Astrophysics Data System (ADS)

Augustins, G.; Etienne, L.; Ferdy, J.-B.; Ferrer, R.; Godelle, B.; Pitard, E.; Rousset, F.

2014-03-01

Reproductive success and survival are influenced by wealth in human populations. Wealth is transmitted to offsprings and strategies of transmission vary over time and among populations, the main variation being how equally wealth is transmitted to children. Here we propose a model where we simulate both the dynamics of wealth in a population and the evolution of a trait that determines how wealth is transmitted from parents to offspring, in a darwinian context.

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Natural selection and the predictability of evolution in Timema stick insects.

PubMed

Nosil, Patrik; Villoutreix, Romain; de Carvalho, Clarissa F; Farkas, Timothy E; Soria-Carrasco, Víctor; Feder, Jeffrey L; Crespi, Bernard J; Gompert, Zach

2018-02-16

Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time ( r 2 = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection ( r 2 = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Selective sweeps of mitochondrial DNA can drive the evolution of uniparental inheritance.

PubMed

Christie, Joshua R; Beekman, Madeleine

2017-08-01

Although the uniparental (or maternal) inheritance of mitochondrial DNA (mtDNA) is widespread, the reasons for its evolution remain unclear. Two main hypotheses have been proposed: selection against individuals containing different mtDNAs (heteroplasmy) and selection against "selfish" mtDNA mutations. Recently, uniparental inheritance was shown to promote adaptive evolution in mtDNA, potentially providing a third hypothesis for its evolution. Here, we explore this hypothesis theoretically and ask if the accumulation of beneficial mutations provides a sufficient fitness advantage for uniparental inheritance to invade a population in which mtDNA is inherited biparentally. In a deterministic model, uniparental inheritance increases in frequency but cannot replace biparental inheritance if only a single beneficial mtDNA mutation sweeps through the population. When we allow successive selective sweeps of mtDNA, however, uniparental inheritance can replace biparental inheritance. Using a stochastic model, we show that a combination of selection and drift facilitates the fixation of uniparental inheritance (compared to a neutral trait) when there is only a single selective mtDNA sweep. When we consider multiple mtDNA sweeps in a stochastic model, uniparental inheritance becomes even more likely to replace biparental inheritance. Our findings thus suggest that selective sweeps of beneficial mtDNA haplotypes can drive the evolution of uniparental inheritance. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Toward an evolutionary-predictive foundation for creativity : Commentary on "Human creativity, evolutionary algorithms, and predictive representations: The mechanics of thought trials" by Arne Dietrich and Hilde Haider, 2014 (Accepted pending minor revisions for publication in Psychonomic Bulletin & Review).

PubMed

Gabora, Liane; Kauffman, Stuart

2016-04-01

Dietrich and Haider (Psychonomic Bulletin & Review, 21 (5), 897-915, 2014) justify their integrative framework for creativity founded on evolutionary theory and prediction research on the grounds that "theories and approaches guiding empirical research on creativity have not been supported by the neuroimaging evidence." Although this justification is controversial, the general direction holds promise. This commentary clarifies points of disagreement and unresolved issues, and addresses mis-applications of evolutionary theory that lead the authors to adopt a Darwinian (versus Lamarckian) approach. To say that creativity is Darwinian is not to say that it consists of variation plus selection - in the everyday sense of the term - as the authors imply; it is to say that evolution is occurring because selection is affecting the distribution of randomly generated heritable variation across generations. In creative thought the distribution of variants is not key, i.e., one is not inclined toward idea A because 60 % of one's candidate ideas are variants of A while only 40 % are variants of B; one is inclined toward whichever seems best. The authors concede that creative variation is partly directed; however, the greater the extent to which variants are generated non-randomly, the greater the extent to which the distribution of variants can reflect not selection but the initial generation bias. Since each thought in a creative process can alter the selective criteria against which the next is evaluated, there is no demarcation into generations as assumed in a Darwinian model. We address the authors' claim that reduced variability and individuality are more characteristic of Lamarckism than Darwinian evolution, and note that a Lamarckian approach to creativity has addressed the challenge of modeling the emergent features associated with insight.

A Lesson on Evolution & Natural Selection

ERIC Educational Resources Information Center

Curtis, Anthony D.

2010-01-01

I describe three activities that allow students to explore the ideas of evolution, natural selection, extinction, mass extinction, and rates of evolutionary change by engaging a simple model using paper, pens, chalk, and a chalkboard. As a culminating activity that supports expository writing in the sciences, the students write an essay on mass…

Sexual selection drives evolution and rapid turnover of male gene expression.

PubMed

Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Dean, Rebecca; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

2015-04-07

The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.

Evolution of Life and SETI (Evo-SETI)

NASA Astrophysics Data System (ADS)

Maccone, Claudio

When SETI scientists will be able to discover a signal or just some signs of an Extra-Terrestrial (ET) Civilization, those ETs should turn out to be technologically advanced at least as much as Humans, if not more, or much more so. Comparing the technological level of two different Civilizations is then a key issue in SETI. But at the moment we only know about the development of life on Earth over the last 3.5 billion years. We thus need to mathematically model the evolution of life on Earth (RNA to Humans) and then apply our results to other extra-solar planets to find out “where they stand” along their evolution of life. In a series of recent papers and in a book (refs. [1] through [4]) this author introduced a new statistical model embracing SETI, Darwinian Evolution and Human History into a unified statistical picture and concisely called Evo-SETI (Evolution & SETI). The relevant mathematical instruments are: 1) The statistical generalization of the Drake equation yielding the number N of communicating ET civilizations in the Galaxy. Assuming that each input variable in the Drake equation was a random variable, rather than just a pure number, N was shown to follow the lognormal probability distribution having as mean value the sum of the input mean values, and as variance the sum of the input variances (ref. [1]). 2) Geometric Brownian Motion (GBM), the stochastic process representing Evolution as the stochastic increase of the number of Species living on Earth over the last 3.5 billion years. This GBM is well-known in the mathematics of finances (Black-Sholes models). Its main features are that its probability density function (pdf) is a lognormal pdf, and its mean value is either an increasing, or, more rarely (as in the Mass Extinctions of the past) a decreasing exponential of the time. 3) The probability distributions known as b-lognormals, i.e. lognormals starting at a certain positive instant b>0 rather than at the origin. These b-lognormals were then

Evolution of genetic architecture under directional selection.

PubMed

Hansen, Thomas F; Alvarez-Castro, José M; Carter, Ashley J R; Hermisson, Joachim; Wagner, Günter P

2006-08-01

We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis.

“The Two Brothers”: Reconciling Perceptual-Cognitive and Statistical Models of Musical Evolution

PubMed Central

Jan, Steven

2018-01-01

While the “units, events and dynamics” of memetic evolution have been abstractly theorized (Lynch, 1998), they have not been applied systematically to real corpora in music. Some researchers, convinced of the validity of cultural evolution in more than the metaphorical sense adopted by much musicology, but perhaps skeptical of some or all of the claims of memetics, have attempted statistically based corpus-analysis techniques of music drawn from molecular biology, and these have offered strong evidence in favor of system-level change over time (Savage, 2017). This article argues that such statistical approaches, while illuminating, ignore the psychological realities of music-information grouping, the transmission of such groups with varying degrees of fidelity, their selection according to relative perceptual-cognitive salience, and the power of this Darwinian process to drive the systemic changes (such as the development over time of systems of tonal organization in music) that statistical methodologies measure. It asserts that a synthesis between such statistical approaches to the study of music-cultural change and the theory of memetics as applied to music (Jan, 2007), in particular the latter's perceptual-cognitive elements, would harness the strengths of each approach and deepen understanding of cultural evolution in music. PMID:29670551

A computational model of selection by consequences.

PubMed

McDowell, J J

2004-05-01

Darwinian selection by consequences was instantiated in a computational model that consisted of a repertoire of behaviors undergoing selection, reproduction, and mutation over many generations. The model in effect created a digital organism that emitted behavior continuously. The behavior of this digital organism was studied in three series of computational experiments that arranged reinforcement according to random-interval (RI) schedules. The quantitative features of the model were varied over wide ranges in these experiments, and many of the qualitative features of the model also were varied. The digital organism consistently showed a hyperbolic relation between response and reinforcement rates, and this hyperbolic description of the data was consistently better than the description provided by other, similar, function forms. In addition, the parameters of the hyperbola varied systematically with the quantitative, and some of the qualitative, properties of the model in ways that were consistent with findings from biological organisms. These results suggest that the material events responsible for an organism's responding on RI schedules are computationally equivalent to Darwinian selection by consequences. They also suggest that the computational model developed here is worth pursuing further as a possible dynamic account of behavior.

A computational model of selection by consequences.

PubMed Central

McDowell, J J

2004-01-01

Darwinian selection by consequences was instantiated in a computational model that consisted of a repertoire of behaviors undergoing selection, reproduction, and mutation over many generations. The model in effect created a digital organism that emitted behavior continuously. The behavior of this digital organism was studied in three series of computational experiments that arranged reinforcement according to random-interval (RI) schedules. The quantitative features of the model were varied over wide ranges in these experiments, and many of the qualitative features of the model also were varied. The digital organism consistently showed a hyperbolic relation between response and reinforcement rates, and this hyperbolic description of the data was consistently better than the description provided by other, similar, function forms. In addition, the parameters of the hyperbola varied systematically with the quantitative, and some of the qualitative, properties of the model in ways that were consistent with findings from biological organisms. These results suggest that the material events responsible for an organism's responding on RI schedules are computationally equivalent to Darwinian selection by consequences. They also suggest that the computational model developed here is worth pursuing further as a possible dynamic account of behavior. PMID:15357512

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

PubMed Central

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-01-01

Abstract Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. PMID:28685813

Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny

PubMed Central

Martínez-Castilla, León Patricio; Alvarez-Buylla, Elena R.

2003-01-01

Gene duplication is a substrate of evolution. However, the relative importance of positive selection versus relaxation of constraints in the functional divergence of gene copies is still under debate. Plant MADS-box genes encode transcriptional regulators key in various aspects of development and have undergone extensive duplications to form a large family. We recovered 104 MADS sequences from the Arabidopsis genome. Bayesian phylogenetic trees recover type II lineage as a monophyletic group and resolve a branching sequence of monophyletic groups within this lineage. The type I lineage is comprised of several divergent groups. However, contrasting gene structure and patterns of chromosomal distribution between type I and II sequences suggest that they had different evolutionary histories and support the placement of the root of the gene family between these two groups. Site-specific and site-branch analyses of positive Darwinian selection (PDS) suggest that different selection regimes could have affected the evolution of these lineages. We found evidence for PDS along the branch leading to flowering time genes that have a direct impact on plant fitness. Sites with high probabilities of having been under PDS were found in the MADS and K domains, suggesting that these played important roles in the acquisition of novel functions during MADS-box diversification. Detected sites are targets for further experimental analyses. We argue that adaptive changes in MADS-domain protein sequences have been important for their functional divergence, suggesting that changes within coding regions of transcriptional regulators have influenced phenotypic evolution of plants. PMID:14597714

Interaction-based evolution: how natural selection and nonrandom mutation work together.

PubMed

Livnat, Adi

2013-10-18

The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation-while not Lamarckian, or "directed" to increase fitness-is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination's fitness. This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional theory can actually experience selection on interactions and thus has a much greater adaptive

Interaction-based evolution: how natural selection and nonrandom mutation work together

PubMed Central

2013-01-01

Background The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Presentation of the hypothesis Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation—while not Lamarckian, or “directed” to increase fitness—is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination’s fitness. Testing and implications of the hypothesis This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional

Drug concentration heterogeneity facilitates the evolution of drug resistance.

PubMed

Kepler, T B; Perelson, A S

1998-09-29

Pathogenic microorganisms use Darwinian processes to circumvent attempts at their control through chemotherapy. In the case of HIV-1 infection, in which drug resistance is a continuing problem, we show that in one-compartment systems, there is a relatively narrow window of drug concentrations that allows evolution of resistant variants. When the system is enlarged to two spatially distinct compartments held at different drug concentrations with transport of virus between them, the range of average drug concentrations that allow evolution of resistance is significantly increased. For high average drug concentrations, resistance is very unlikely to arise without spatial heterogeneity. We argue that a quantitative understanding of the role played by heterogeneity in drug levels and pathogen transport is crucial for attempts to control re-emergent infectious disease.

[Social institutions and tempering of affects as "contraints" of social change. Norbert Elias' theory on the civilization theory in light of the biologic system theory of evolution].

PubMed

Weinich, Detlef

2005-01-01

This study is to be regarded as a contribution to interdisciplinary research and represents an attempt to clarify the question of whether and to what extent concepts that have been developed in the field of theoretical biology and which have a high degree of importance here can also be applied to sociological phenomena. In particular it is intended to examine the question of whether the civilizing process can be adequately treated using the evolutionary concept of "Constraints". This term, which has only recently been introduced into the discussion by PERE ALBERCH as an evolutionary factor, comprises all of the internal factors which influence the further course of the evolution of a system by ruling out certain possibilities, thus showing a limiting effect. Although "Constraints" go beyond the scope of Darwinian teachings about selection by the environment, they are increasingly accepted today as evolution factors by well-known exponents of Darwinian theory (cf. MAYNARD-SMITH 1985). The increase in popularity of "constraints" is also an expression of the rediscovery of a phenomenon which was originally expressed by RUPERT RIEDL and was introduced by him into German literature in the seventies. In the clarification of this question, special reference is made to the "theory of the civilizing process" by NORBERT ELIAS, since here a highly respected scholar has presented an important sociological theory. Moreover, there is such good scientific access to ELIAS because this author exemplifies his theses in historical terms and thus to a certain extent makes his explanations verifiable in scientific terms. In the treatment of this topic, the central terms and theses of ELIAS will be presented from the considerable scope of his work, and then illustrated with the help of several selected historical case studies. Furthermore, reference will be made at the relevant points to parallels and analogies which the works of ELIAS have to other, predominantly system

Unnatural selection in chemical systems

NASA Technical Reports Server (NTRS)

Orgel, Leslie E.

1995-01-01

The theory of evolution through natural selection was proposed by Darwin and Wallace to explain how the characteristics of populations of animals change with time. An examination of their assumptions shows that the theory has much broader application than they originally envisaged. We now know that in appropriate environments RNA molecules or computer viruses, for example, can evolve. The adventure with which we are concerned is the quest for chemical systems that undergo processes analogous to Darwinian selection in the test tube. The search is not restricted to systems that are closely related to nucleic acids, although most of the available experimental evidence concerns such systems. A population of molecules satisfies all the requirements of the theory is there are different kinds of molecules in the population and if each individual molecule can direct the formation of copies of itself, then a population of molecules will adapt to a varying environment by changing its composition so as to maintain as high as possible a rate of replication. Sol Spiegelman is the inventor of 'unnatural selection'. He showed clearly that populations of RNA molecules evolve when replicated repeatedly by Q beta RNA polymerase under a chosen set of adverse reaction conditions. In the systems that he studied, the initial population was fairly homogeneous and much of the variation was created during the course of the experiment by mutation, that is, error of replication. The term 'unnatural selection' will be used loosely to describe evolution of nucleic acids or other replicatable polymers in vitro. The term 'Natural Selection' will be reserved for the evolution of living organisms and their viruses. Natural Section usually involves the coevolution of nucleic acids and proteins, while 'unnatural selection', as practiced so far, allows replicating nucleic acids to evolve but hold constant the enzymes that catalyze replication. It is widely believed that biology based on DNA, RNA, and

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems

PubMed Central

Ruiz-Mirazo, Kepa; Briones, Carlos

2017-01-01

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. PMID:28446711

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems.

PubMed

Ruiz-Mirazo, Kepa; Briones, Carlos; de la Escosura, Andrés

2017-04-01

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. © 2017 The Authors.

The Evolution of Biological Complexity in Digital Organisms

NASA Astrophysics Data System (ADS)

Ofria, Charles

2013-03-01

When Darwin first proposed his theory of evolution by natural selection, he realized that it had a problem explaining the origins of traits of ``extreme perfection and complication'' such as the vertebrate eye. Critics of Darwin's theory have latched onto this perceived flaw as a proof that Darwinian evolution is impossible. In anticipation of this issue, Darwin described the perfect data needed to understand this process, but lamented that such data are ``scarcely ever possible'' to obtain. In this talk, I will discuss research where we use populations of digital organisms (self-replicating and evolving computer programs) to elucidate the genetic and evolutionary processes by which new, highly-complex traits arise, drawing inspiration directly from Darwin's wistful thinking and hypotheses. During the process of evolution in these fully-transparent computational environments we can measure the incorporation of new information into the genome, a process akin to a natural Maxwell's Demon, and identify the original source of any such information. We show that, as Darwin predicted, much of the information used to encode a complex trait was already in the genome as part of simpler evolved traits, and that many routes must be possible for a new complex trait to have a high probability of successfully evolving. In even more extreme examples of the evolution of complexity, we are now using these same principles to examine the evolutionary dynamics the drive major transitions in evolution; that is transitions to higher-levels of organization, which are some of the most complex evolutionary events to occur in nature. Finally, I will explore some of the implications of this research to other aspects of evolutionary biology and as well as ways that these evolutionary principles can be applied toward solving computational and engineering problems.

Adaptive evolution in locomotor performance: How selective pressures and functional relationships produce diversity.

PubMed

Scales, Jeffrey A; Butler, Marguerite A

2016-01-01

Despite the complexity of nature, most comparative studies of phenotypic evolution consider selective pressures in isolation. When competing pressures operate on the same system, it is commonly expected that trade-offs will occur that will limit the evolution of phenotypic diversity, however, it is possible that interactions among selective pressures may promote diversity instead. We explored the evolution of locomotor performance in lizards in relation to possible selective pressures using the Ornstein-Uhlenbeck process. Here, we show that a combination of selection based on foraging mode and predator escape is required to explain variation in performance phenotypes. Surprisingly, habitat use contributed little explanatory power. We find that it is possible to evolve very different abilities in performance which were previously thought to be tightly correlated, supporting a growing literature that explores the many-to-one mapping of morphological design. Although we generally find the expected trade-off between maximal exertion and speed, this relationship surprisingly disappears when species experience selection for both performance types. We conclude that functional integration need not limit adaptive potential, and that an integrative approach considering multiple major influences on a phenotype allows a more complete understanding of adaptation and the evolution of diversity. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Postcopulatory sexual selection influences baculum evolution in primates and carnivores.

PubMed

Brindle, Matilda; Opie, Christopher

2016-12-14

The extreme morphological variability of the baculum across mammals is thought to be the result of sexual selection (particularly, high levels of postcopulatory selection). However, the evolutionary trajectory of the mammalian baculum is little studied and evidence for the adaptive function of the baculum has so far been elusive. Here, we use Markov chain Monte Carlo methods implemented in a Bayesian phylogenetic framework to reconstruct baculum evolution across the mammalian class and investigate the rate of baculum length evolution within the primate order. We then test the effects of testes mass (postcopulatory sexual selection), polygamy, seasonal breeding and intromission duration on the baculum in primates and carnivores. The ancestral mammal did not have a baculum, but both ancestral primates and carnivores did. No relationship was found between testes mass and baculum length in either primates or carnivores. Intromission duration correlated with baculum presence over the course of primate evolution, and prolonged intromission predicts significantly longer bacula in extant primates and carnivores. Both polygamous and seasonal breeding systems predict significantly longer bacula in primates. These results suggest the baculum plays an important role in facilitating reproductive strategies in populations with high levels of postcopulatory sexual selection. © 2016 The Authors.

Postcopulatory sexual selection influences baculum evolution in primates and carnivores

PubMed Central

Brindle, Matilda

2016-01-01

The extreme morphological variability of the baculum across mammals is thought to be the result of sexual selection (particularly, high levels of postcopulatory selection). However, the evolutionary trajectory of the mammalian baculum is little studied and evidence for the adaptive function of the baculum has so far been elusive. Here, we use Markov chain Monte Carlo methods implemented in a Bayesian phylogenetic framework to reconstruct baculum evolution across the mammalian class and investigate the rate of baculum length evolution within the primate order. We then test the effects of testes mass (postcopulatory sexual selection), polygamy, seasonal breeding and intromission duration on the baculum in primates and carnivores. The ancestral mammal did not have a baculum, but both ancestral primates and carnivores did. No relationship was found between testes mass and baculum length in either primates or carnivores. Intromission duration correlated with baculum presence over the course of primate evolution, and prolonged intromission predicts significantly longer bacula in extant primates and carnivores. Both polygamous and seasonal breeding systems predict significantly longer bacula in primates. These results suggest the baculum plays an important role in facilitating reproductive strategies in populations with high levels of postcopulatory sexual selection. PMID:27974519

Defining Life

PubMed Central

2010-01-01

Abstract Any definition is intricately connected to a theory that gives it meaning. Accordingly, this article discusses various definitions of life held in the astrobiology community by considering their connected “theories of life.” These include certain “list” definitions and a popular definition that holds that life is a “self-sustaining chemical system capable of Darwinian evolution.” We then act as “anthropologists,” studying what scientists do to determine which definition-theories of life they constructively hold as they design missions to seek non-terran life. We also look at how constructive beliefs about biosignatures change as observational data accumulate. And we consider how a definition centered on Darwinian evolution might itself be forced to change as supra-Darwinian species emerge, including in our descendents, and consider the chances of our encountering supra-Darwinian species in our exploration of the Cosmos. Last, we ask what chemical structures might support Darwinian evolution universally; these structures might be universal biosignatures. Key Words: Evolution—Life—Life detection—Biosignatures. Astrobiology 10, 1021–1030. PMID:21162682

Adaptations to sexual selection and sexual conflict: insights from experimental evolution and artificial selection.

PubMed

Edward, Dominic A; Fricke, Claudia; Chapman, Tracey

2010-08-27

Artificial selection and experimental evolution document natural selection under controlled conditions. Collectively, these techniques are continuing to provide fresh and important insights into the genetic basis of evolutionary change, and are now being employed to investigate mating behaviour. Here, we focus on how selection techniques can reveal the genetic basis of post-mating adaptations to sexual selection and sexual conflict. Alteration of the operational sex ratio of adult Drosophila over just a few tens of generations can lead to altered ejaculate allocation patterns and the evolution of resistance in females to the costly effects of elevated mating rates. We provide new data to show how male responses to the presence of rivals can evolve. For several traits, the way in which males responded to rivals was opposite in lines selected for male-biased, as opposed to female-biased, adult sex ratio. This shows that the manipulation of the relative intensity of intra- and inter-sexual selection can lead to replicable and repeatable effects on mating systems, and reveals the potential for significant contemporary evolutionary change. Such studies, with important safeguards, have potential utility for understanding sexual selection and sexual conflict across many taxa. We discuss how artificial selection studies combined with genomics will continue to deepen our knowledge of the evolutionary principles first laid down by Darwin 150 years ago.

A Darwinian approach to the origin of life cycles with group properties.

PubMed

Rashidi, Armin; Shelton, Deborah E; Michod, Richard E

2015-06-01

A selective explanation for the evolution of multicellular organisms from unicellular ones requires knowledge of both selective pressures and factors affecting the response to selection. Understanding the response to selection is particularly challenging in the case of evolutionary transitions in individuality, because these transitions involve a shift in the very units of selection. We develop a conceptual framework in which three fundamental processes (growth, division, and splitting) are the scaffold for unicellular and multicellular life cycles alike. We (i) enumerate the possible ways in which these processes can be linked to create more complex life cycles, (ii) introduce three genes based on growth, division and splitting that, acting in concert, determine the architecture of the life cycles, and finally, (iii) study the evolution of the simplest five life cycles using a heuristic model of coupled ordinary differential equations in which mutations are allowed in the three genes. We demonstrate how changes in the regulation of three fundamental aspects of colonial form (cell size, colony size, and colony cell number) could lead unicellular life cycles to evolve into primitive multicellular life cycles with group properties. One interesting prediction of the model is that selection generally favors cycles with group level properties when intermediate body size is associated with lowest mortality. That is, a universal requirement for the evolution of group cycles in the model is that the size-mortality curve be U-shaped. Furthermore, growth must decelerate with size. Copyright © 2015 Elsevier Inc. All rights reserved.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

PubMed

Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Darwinian sex roles confirmed across the animal kingdom

PubMed Central

Janicke, Tim; Häderer, Ines K.; Lajeunesse, Marc J.; Anthes, Nils

2016-01-01

Since Darwin’s conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental factors or chance. We demonstrate that, across the animal kingdom, sexual selection, as captured by standard Bateman metrics, is indeed stronger in males than in females and that it is evolutionarily tied to sex biases in parental care and sexual dimorphism. Our findings provide the first comprehensive evidence that Darwin’s concept of conventional sex roles is accurate and refute recent criticism of sexual selection theory. PMID:26933680

Darwinian sex roles confirmed across the animal kingdom.

PubMed

Janicke, Tim; Häderer, Ines K; Lajeunesse, Marc J; Anthes, Nils

2016-02-01

Since Darwin's conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental factors or chance. We demonstrate that, across the animal kingdom, sexual selection, as captured by standard Bateman metrics, is indeed stronger in males than in females and that it is evolutionarily tied to sex biases in parental care and sexual dimorphism. Our findings provide the first comprehensive evidence that Darwin's concept of conventional sex roles is accurate and refute recent criticism of sexual selection theory.

Paleontology and Darwin's Theory of Evolution: The Subversive Role of Statistics at the End of the 19th Century.

PubMed

Tamborini, Marco

2015-11-01

This paper examines the subversive role of statistics paleontology at the end of the 19th and the beginning of the 20th centuries. In particular, I will focus on German paleontology and its relationship with statistics. I argue that in paleontology, the quantitative method was questioned and strongly limited by the first decade of the 20th century because, as its opponents noted, when the fossil record is treated statistically, it was found to generate results openly in conflict with the Darwinian theory of evolution. Essentially, statistics questions the gradual mode of evolution and the role of natural selection. The main objections to statistics were addressed during the meetings at the Kaiserlich-Königliche Geologische Reichsanstalt in Vienna in the 1880s. After having introduced the statistical treatment of the fossil record, I will use the works of Charles Léo Lesquereux (1806-1889), Joachim Barrande (1799-1833), and Henry Shaler Williams (1847-1918) to compare the objections raised in Vienna with how the statistical treatment of the data worked in practice. Furthermore, I will discuss the criticisms of Melchior Neumayr (1845-1890), one of the leading German opponents of statistical paleontology, to show why, and to what extent, statistics were questioned in Vienna. The final part of this paper considers what paleontologists can derive from a statistical notion of data: the necessity of opening a discussion about the completeness and nature of the paleontological data. The Vienna discussion about which method paleontologists should follow offers an interesting case study in order to understand the epistemic tensions within paleontology surrounding Darwin's theory as well as the variety of non-Darwinian alternatives that emerged from the statistical treatment of the fossil record at the end of the 19th century.

Conceptualizing the origin of life in terms of evolution

NASA Astrophysics Data System (ADS)

Takeuchi, N.; Hogeweg, P.; Kaneko, K.

2017-11-01

In this opinion piece, we discuss how to place evolution in the context of origin-of-life research. Our discussion starts with a popular definition: `life is a self-sustained chemical system capable of undergoing Darwinian evolution'. According to this definition, the origin of life is the same as the origin of evolution: evolution is the `end' of the origin of life. This perspective, however, has a limitation, in that the ability of evolution in and of itself is insufficient to explain the origin of life as we know it, as indicated by Spiegelman's and Lincoln and Joyce's experiments. This limitation provokes a crucial question: What conditions are required for replicating systems to evolve into life? From this perspective, the origin of life includes the emergence of life through evolution: evolution is a `means' of the origin of life. After reviewing Eigen's pioneering work on this question, we mention our ongoing work suggesting that a key condition might be conflicting multi-level evolution. Taken together, there are thus two questions regarding the origin of life: how evolution gets started, and how evolution produces life. Evolution is, therefore, at the centre of the origin of life, where the two lines of enquiry must meet. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Positive selection drives faster-Z evolution in silkmoths

PubMed Central

Sackton, Timothy B.; Corbett-Detig, Russell B.; Nagaraju, Javaregowda; Vaishna, R. Lakshmi; Arunkumar, Kallare P.; Hartl, Daniel L.

2014-01-01

Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This “faster-X effect” can arise either as a consequence of hemizygosity, which leads to more efficient selection for recessive beneficial mutations in the heterogametic sex, or as a consequence of reduced effective population size of the hemizygous chromosome, which leads to increased fixation of weakly deleterious mutations due to genetic drift. Empirical results to date suggest that, while the overall pattern across taxa is complicated, systems with male-heterogamy show a faster-X effect attributable to more efficient selection, while the faster-Z effect in female-heterogametic taxa is attributable to increased drift. To test the generality of the faster-Z pattern seen in birds and snakes, we sequenced the genome of the Lepidopteran silkmoth Bombyx huttoni. We show that silkmoths experience faster-Z evolution, but unlike in birds and snakes, the faster-Z effect appears to be attributable to more efficient positive selection. These results suggest that female-heterogamy alone is unlikely to explain the reduced efficacy of selection on the bird Z chromosome. It is likely that many factors, including differences in overall effective population size, influence Z chromosome evolution. PMID:24826901

Darwinism and the cultural evolution of sports.

PubMed

De Block, Andreas; Dewitte, Siegfried

2009-01-01

This article outlines a Darwinian approach to sports that takes into account its profoundly cultural character and thereby overcomes the traditional nature-culture dichotomies in the sociology of sport. We argue that there are good reasons to view sports as culturally evolved signaling systems that serve a function similar to (biological) courtship rituals in other animals. Our approach combines the insights of evolutionary psychology, which states that biological adaptations determine the boundaries for the types of sport that are possible, and pure cultural theories, which describe the mechanism of cultural evolution without referring to sport's biological bases. Several biological and cultural factors may moderate the direct effect that signaling value has on a sport's viability or popularity. Social learning underlies many aspects of the cultural control of sports, and sports have evolved new cultural functions more-or-less unrelated to mate choice as cultural evolution itself became important in humans.

Evidence of size-selective evolution in the fighting conch from prehistoric subsistence harvesting.

PubMed

O'Dea, Aaron; Shaffer, Marian Lynne; Doughty, Douglas R; Wake, Thomas A; Rodriguez, Felix A

2014-05-07

Intensive size-selective harvesting can drive evolution of sexual maturity at smaller body size. Conversely, prehistoric, low-intensity subsistence harvesting is not considered an effective agent of size-selective evolution. Uniting archaeological, palaeontological and contemporary material, we show that size at sexual maturity in the edible conch Strombus pugilis declined significantly from pre-human (approx. 7 ka) to prehistoric times (approx. 1 ka) and again to the present day. Size at maturity also fell from early- to late-prehistoric periods, synchronous with an increase in harvesting intensity as other resources became depleted. A consequence of declining size at maturity is that early prehistoric harvesters would have received two-thirds more meat per conch than contemporary harvesters. After exploring the potential effects of selection biases, demographic shifts, environmental change and habitat alteration, these observations collectively implicate prehistoric subsistence harvesting as an agent of size-selective evolution with long-term detrimental consequences. We observe that contemporary populations that are protected from harvesting are slightly larger at maturity, suggesting that halting or even reversing thousands of years of size-selective evolution may be possible.

Evidence of size-selective evolution in the fighting conch from prehistoric subsistence harvesting

PubMed Central

O'Dea, Aaron; Shaffer, Marian Lynne; Doughty, Douglas R.; Wake, Thomas A.; Rodriguez, Felix A.

2014-01-01

Intensive size-selective harvesting can drive evolution of sexual maturity at smaller body size. Conversely, prehistoric, low-intensity subsistence harvesting is not considered an effective agent of size-selective evolution. Uniting archaeological, palaeontological and contemporary material, we show that size at sexual maturity in the edible conch Strombus pugilis declined significantly from pre-human (approx. 7 ka) to prehistoric times (approx. 1 ka) and again to the present day. Size at maturity also fell from early- to late-prehistoric periods, synchronous with an increase in harvesting intensity as other resources became depleted. A consequence of declining size at maturity is that early prehistoric harvesters would have received two-thirds more meat per conch than contemporary harvesters. After exploring the potential effects of selection biases, demographic shifts, environmental change and habitat alteration, these observations collectively implicate prehistoric subsistence harvesting as an agent of size-selective evolution with long-term detrimental consequences. We observe that contemporary populations that are protected from harvesting are slightly larger at maturity, suggesting that halting or even reversing thousands of years of size-selective evolution may be possible. PMID:24648229

Progress in life's history: Linking Darwinism and palaeontology in Britain, 1860-1914.

PubMed

Manias, Chris

2017-12-01

This paper examines the tension between Darwinian evolution and palaeontological research in Britain in the 1860-1914 period, looking at how three key promoters of Darwinian thinking - Thomas Henry Huxley, Edwin Ray Lankester and Alfred Russell Wallace - integrated palaeontological ideas and narratives of life's history into their public presentations of evolutionary theory. It shows how engagement with palaeontological science was an important part of the promotion of evolutionary ideas in Britain, which often bolstered notions that evolution depended upon progress and development along a wider plan. While often critical of some of the non-Darwinian concepts of evolution professed by many contemporary palaeontologists, and frequently citing the 'imperfection' of the fossil record itself, Darwinian thinkers nevertheless engaged extensively with palaeontology to develop evolutionary narratives informed by notions of improvement and progress within the natural world. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Evolution in population parameters: density-dependent selection or density-dependent fitness?

PubMed

Travis, Joseph; Leips, Jeff; Rodd, F Helen

2013-05-01

Density-dependent selection is one of earliest topics of joint interest to both ecologists and evolutionary biologists and thus occupies an important position in the histories of these disciplines. This joint interest is driven by the fact that density-dependent selection is the simplest form of feedback between an ecological effect of an organism's own making (crowding due to sustained population growth) and the selective response to the resulting conditions. This makes density-dependent selection perhaps the simplest process through which we see the full reciprocity between ecology and evolution. In this article, we begin by tracing the history of studying the reciprocity between ecology and evolution, which we see as combining the questions of evolutionary ecology with the assumptions and approaches of ecological genetics. In particular, density-dependent fitness and density-dependent selection were critical concepts underlying ideas about adaptation to biotic selection pressures and the coadaptation of interacting species. However, theory points to a critical distinction between density-dependent fitness and density-dependent selection in their influences on complex evolutionary and ecological interactions among coexisting species. Although density-dependent fitness is manifestly evident in empirical studies, evidence of density-dependent selection is much less common. This leads to the larger question of how prevalent and important density-dependent selection might really be. Life-history variation in the least killifish Heterandria formosa appears to reflect the action of density-dependent selection, and yet compelling evidence is elusive, even in this well-studied system, which suggests some important challenges for understanding density-driven feedbacks between ecology and evolution.

Evolution of divergent female mating preference in response to experimental sexual selection.

PubMed

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-09-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

The search for purpose in a post-Darwinian universe: George Bernard Shaw, 'creative evolution', and Shavian eugenics: 'The dark side of the force'.

PubMed

Hale, Piers J

2006-01-01

The Irish playwright and socialist George Bernard Shaw has been of marginal concern for historians of biology because his vitalist Lamarckism has been viewed as out of step with contemporary science. However, Julian Huxley and J.B.S. Haldane were certainly of the opinion that Shaw was a man of influence in this regard and took pains to counter his views in their own attempts to engage the public in science. Previously, Shaw's colleague and friend H.G. Wells had also agued with Shaw from his own mechanistic neo-Darwinian perspective. The very public debate between Shaw and Wells, which continued to concern Huxley and Haldane, shows that public concern over the moral implications of Darwinism has a long history. Taking into account the opinions of John Maynard Smith on this matter, I suggest that a consideration of Shaw in this context can give us an understanding of the historical popularity of vitalist teleology as well as of the persistent ambivalence to the non-normative character of Darwinism.

How sexual selection can drive the evolution of costly sperm ornamentation

NASA Astrophysics Data System (ADS)

Lüpold, Stefan; Manier, Mollie K.; Puniamoorthy, Nalini; Schoff, Christopher; Starmer, William T.; Luepold, Shannon H. Buckley; Belote, John M.; Pitnick, Scott

2016-05-01

Post-copulatory sexual selection (PSS), fuelled by female promiscuity, is credited with the rapid evolution of sperm quality traits across diverse taxa. Yet, our understanding of the adaptive significance of sperm ornaments and the cryptic female preferences driving their evolution is extremely limited. Here we review the evolutionary allometry of exaggerated sexual traits (for example, antlers, horns, tail feathers, mandibles and dewlaps), show that the giant sperm of some Drosophila species are possibly the most extreme ornaments in all of nature and demonstrate how their existence challenges theories explaining the intensity of sexual selection, mating-system evolution and the fundamental nature of sex differences. We also combine quantitative genetic analyses of interacting sex-specific traits in D. melanogaster with comparative analyses of the condition dependence of male and female reproductive potential across species with varying ornament size to reveal complex dynamics that may underlie sperm-length evolution. Our results suggest that producing few gigantic sperm evolved by (1) Fisherian runaway selection mediated by genetic correlations between sperm length, the female preference for long sperm and female mating frequency, and (2) longer sperm increasing the indirect benefits to females. Our results also suggest that the developmental integration of sperm quality and quantity renders post-copulatory sexual selection on ejaculates unlikely to treat male-male competition and female choice as discrete processes.

Evolution of male and female genitalia following release from sexual selection.

PubMed

Cayetano, Luis; Maklakov, Alexei A; Brooks, Robert C; Bonduriansky, Russell

2011-08-01

Despite the key functions of the genitalia in sexual interactions and fertilization, the role of sexual selection and conflict in shaping genital traits remains poorly understood. Seed beetle (Callosobruchus maculatus) males possess spines on the intromittent organ, and females possess a thickened reproductive tract wall that also bears spines. We investigated the role of sexual selection and conflict by imposing monogamous mating on eight replicate populations of this naturally polygamous insect, while maintaining eight other populations under polygamy. To establish whether responses to mating system manipulation were robust to ecological context, we simultaneously manipulated life-history selection (early/late reproduction). Over 18-21 generations, male genital spines evolved relatively reduced length in large males (i.e., shallower static allometry) in monogamous populations. Two nonintromittent male genital appendages also evolved in response to the interaction of mating system and ecology. In contrast, no detectable evolution occurred in female genitalia, consistent with the expectation of a delayed response in defensive traits. Our results support a sexually antagonistic role for the male genital spines, and demonstrate the evolution of static allometry in response to variation in sexual selection opportunity. We argue that further advances in the study of genital coevolution will require a much more detailed understanding of the functions of male and female genital traits. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Sex-biased dispersal, kin selection and the evolution of sexual conflict.

PubMed

Faria, Gonçalo S; Varela, Susana A M; Gardner, Andy

2015-10-01

There is growing interest in resolving the curious disconnect between the fields of kin selection and sexual selection. Rankin's (2011, J. Evol. Biol. 24, 71-81) theoretical study of the impact of kin selection on the evolution of sexual conflict in viscous populations has been particularly valuable in stimulating empirical research in this area. An important goal of that study was to understand the impact of sex-specific rates of dispersal upon the coevolution of male-harm and female-resistance behaviours. But the fitness functions derived in Rankin's study do not flow from his model's assumptions and, in particular, are not consistent with sex-biased dispersal. Here, we develop new fitness functions that do logically flow from the model's assumptions, to determine the impact of sex-specific patterns of dispersal on the evolution of sexual conflict. Although Rankin's study suggested that increasing male dispersal always promotes the evolution of male harm and that increasing female dispersal always inhibits the evolution of male harm, we find that the opposite can also be true, depending upon parameter values. © 2015 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

Controlled evolution of an RNA enzyme

NASA Technical Reports Server (NTRS)

Joyce, G. F.

1991-01-01

It is generally thought that prior to the origin of protein synthesis, life on earth was based on self-replicating RNA molecules. This idea has become especially popular recently due to the discovery of catalytic RNA (ribozymes). RNA has both genotypic and phenotypic properties, suggesting that it is capable of undergoing Darwinian evolution. RNA evolution is likely to have played a critical role in the early history of life on earth, and thus is important in considering the possibility of life elsewhere in the solar system. We have constructed an RNA-based evolving system in the laboratory, combining amplification and mutation of an RNA genotype with selection of a corresponding RNA phenotype. This system serves as a functional model of a primitive organism. It can also be used as a tool to explore the catalytic potential of RNA. By altering the selection constraints, we are attempting to modify the substrate specificity of an existing ribozyme in order to develop ribozymes with novel catalytic function. In this way, we hope to gain a better understanding of RNA's catalytic versatility and to assess its suitability for the role of primordial catalyst. All of the RNA enzymes that are known to exist in contemporary biology carry out cleavage/ligation reactions involving RNA substrates. The Tetrahymena ribozyme, for example, catalyzes phosphoester transfer between a guanosine containing and an oligopyrimidine containing substrate. We tested the ability of mutant forms of the Tetrahymena ribozyme to carry out a comparable reaction using DNA, rather than RNA substrate. An ensemble of structural variants of the ribozyme was prepared and tested for their ability to specifically cleave d(GGCCCTCT-A3TA3TA) at the phosphodiester bond following the sequence CCCTCT. We recovered a mutant form of the enzyme that cleaves DNA more efficiently than does the wild-type. Beginning with this selected mutant we have now scattered random mutations throughout the ribozyme and have begun

Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana.

PubMed

Gossmann, Toni I; Schmid, Marc W; Grossniklaus, Ueli; Schmid, Karl J

2014-03-01

Sex-biased genes are genes with a preferential or specific expression in one sex and tend to show an accelerated rate of evolution in animals. Various hypotheses--which are not mutually exclusive--have been put forth to explain observed patterns of rapid evolution. One possible explanation is positive selection, but this has been shown only in few animal species and mostly for male-specific genes. Here, we present a large-scale study that investigates evolutionary patterns of sex-biased genes in the predominantly self-fertilizing plant Arabidopsis thaliana. Unlike most animal species, A. thaliana does not possess sex chromosomes, its flowers develop both male and female sexual organs, and it is characterized by low outcrossing rates. Using cell-specific gene expression data, we identified genes whose expression is enriched in comparison with all other tissues in the male and female gametes (sperm, egg, and central cell), as well as in synergids, pollen, and pollen tubes, which also play an important role in reproduction. Genes specifically expressed in gametes and synergids show higher rates of protein evolution compared with the genome-wide average and no evidence for positive selection. In contrast, pollen- and pollen tube-specific genes not only have lower rates of protein evolution but also exhibit a higher proportion of adaptive amino acid substitutions. We show that this is the result of increased levels of purifying and positive selection among genes with pollen- and pollen tube-specific expression. The increased proportion of adaptive substitutions cannot be explained by the fact that pollen- and pollen tube-expressed genes are enriched in segmental duplications, are on average older, or have a larger effective population size. Our observations are consistent with prezygotic sexual selection as a result of interactions during pollination and pollen tube growth such as pollen tube competition.

Birds Do It, Bees Do It: Evolution and the Comparative Psychology of Mate Choice

ERIC Educational Resources Information Center

Boothroyd, Lynda G.; McLaughlin, Edward

2011-01-01

The primary theoretical framework for the study of human physical attraction is currently Darwinian sexual selection. Not only has this perspective enabled the discovery of what appear to be strong universals in human mate choice but it has also facilitated our understanding of systematic variation in preferences both between and within…

"Plants that Remind Me of Home": Collecting, Plant Geography, and a Forgotten Expedition in the Darwinian Revolution.

PubMed

Hung, Kuang-Chi

2017-02-01

In 1859, Harvard botanist Asa Gray (1810-1888) published an essay of what he called "the abstract of Japan botany." In it, he applied Charles Darwin's evolutionary theory to explain why strong similarities could be found between the flora of Japan and that of eastern North America, which provoked his famous debate with Louis Agassiz (1807-1873) and initiated Gray's efforts to secure a place for Darwinian biology in the American sciences. Notably, although the Gray-Agassiz debate has become one of the most thoroughly studied scientific debates, historians of science remain unable to answer one critical question: How was Gray able to acquire specimens from Japan? Making use of previously unknown archival materials, this article scrutinizes the institutional, instrumental, financial, and military settings that enabled Gray's collector, Charles Wright (1811-1885), to travel to Japan, as well as examine Wright's collecting practices in Japan. I argue that it is necessary to examine Gray's diagnosis of Japan's flora and the subsequent debate about it from the viewpoint of field sciences. The field-centered approach not only unveils an array of historical significances that have been overshadowed by the analytical framework of the Darwinian revolution and the reception of Darwinism, but also places a seemingly domestic incident in a transnational context.

Complex and changing patterns of natural selection explain the evolution of the human hip.

PubMed

Grabowski, Mark; Roseman, Charles C

2015-08-01

Causal explanations for the dramatic changes that occurred during the evolution of the human hip focus largely on selection for bipedal function and locomotor efficiency. These hypotheses rest on two critical assumptions. The first-that these anatomical changes served functional roles in bipedalism-has been supported in numerous analyses showing how postcranial changes likely affected locomotion. The second-that morphological changes that did play functional roles in bipedalism were the result of selection for that behavior-has not been previously explored and represents a major gap in our understanding of hominin hip evolution. Here we use evolutionary quantitative genetic models to test the hypothesis that strong directional selection on many individual aspects of morphology was responsible for the large differences observed across a sample of fossil hominin hips spanning the Plio-Pleistocene. Our approach uses covariance among traits and the differences between relatively complete fossils to estimate the net selection pressures that drove the major transitions in hominin hip evolution. Our findings show a complex and changing pattern of natural selection drove hominin hip evolution, and that many, but not all, traits hypothesized to play functional roles in bipedalism evolved as a direct result of natural selection. While the rate of evolutionary change for all transitions explored here does not exceed the amount expected if evolution was occurring solely through neutral processes, it was far above rates of evolution for morphological traits in other mammalian groups. Given that stasis is the norm in the mammalian fossil record, our results suggest that large shifts in the adaptive landscape drove hominin evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today.

PubMed

Kutschera, Ulrich

2009-11-01

The book On the Origin of Species, published in November 1859, is an "abstract" without references, compiled by Charles Darwin from a much longer manuscript entitled "Natural Selection." Here, I summarize the five theories that can be extracted from Darwin's monograph, explain the true meaning of the phrase "struggle for life" (i.e., competition and cooperation), and outline Darwin's original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that "selection only eliminates but is not creative" is still alive today. However, I document that August Weismann (Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen (Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this "Weismann-Schmalhausen principle" with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky (Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by prokaryotic microbes. Eubacteria

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.

PubMed

Dean, Rebecca; Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Mank, Judith E

2015-10-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution in fluctuating environments: decomposing selection into additive components of the Robertson-Price equation.

PubMed

Engen, Steinar; Saether, Bernt-Erik

2014-03-01

We analyze the stochastic components of the Robertson-Price equation for the evolution of quantitative characters that enables decomposition of the selection differential into components due to demographic and environmental stochasticity. We show how these two types of stochasticity affect the evolution of multivariate quantitative characters by defining demographic and environmental variances as components of individual fitness. The exact covariance formula for selection is decomposed into three components, the deterministic mean value, as well as stochastic demographic and environmental components. We show that demographic and environmental stochasticity generate random genetic drift and fluctuating selection, respectively. This provides a common theoretical framework for linking ecological and evolutionary processes. Demographic stochasticity can cause random variation in selection differentials independent of fluctuating selection caused by environmental variation. We use this model of selection to illustrate that the effect on the expected selection differential of random variation in individual fitness is dependent on population size, and that the strength of fluctuating selection is affected by how environmental variation affects the covariance in Malthusian fitness between individuals with different phenotypes. Thus, our approach enables us to partition out the effects of fluctuating selection from the effects of selection due to random variation in individual fitness caused by demographic stochasticity. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Genome-wide signals of positive selection in human evolution

PubMed Central

Enard, David; Messer, Philipp W.; Petrov, Dmitri A.

2014-01-01

The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci, and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that many of the candidate loci are false positives and that most genome-wide signatures of adaptation are in fact due to reduction of neutral diversity by linked deleterious mutations, known as background selection. Here we analyze human polymorphism data from the 1000 Genomes Project and detect signatures of positive selection once we correct for the effects of background selection. We show that levels of neutral polymorphism are lower near amino acid substitutions, with the strongest reduction observed specifically near functionally consequential amino acid substitutions. Furthermore, amino acid substitutions are associated with signatures of recent adaptation that should not be generated by background selection, such as unusually long and frequent haplotypes and specific distortions in the site frequency spectrum. We use forward simulations to argue that the observed signatures require a high rate of strongly adaptive substitutions near amino acid changes. We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes. PMID:24619126

Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.

PubMed

Flegr, Jaroslav

2010-01-13

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).

Similarity selection and the evolution of sex: revisiting the red queen.

PubMed

Agrawal, Aneil F

2006-08-01

For over 25 years, many evolutionary ecologists have believed that sexual reproduction occurs because it allows hosts to change genotypes each generation and thereby evade their coevolving parasites. However, recent influential theoretical analyses suggest that, though parasites can select for sex under some conditions, they often select against it. These models assume that encounters between hosts and parasites are completely random. Because of this assumption, the fitness of a host depends only on its own genotype ("genotypic selection"). If a host is even slightly more likely to encounter a parasite transmitted by its mother than expected by random chance, then the fitness of a host also depends on its genetic similarity to its mother ("similarity selection"). A population genetic model is presented here that includes both genotypic and similarity selection, allowing them to be directly compared in the same framework. It is shown that similarity selection is a much more potent force with respect to the evolution of sex than is genotypic selection. Consequently, similarity selection can drive the evolution of sex even if it is much weaker than genotypic selection with respect to fitness. Examination of explicit coevolutionary models reveals that even a small degree of mother-offspring parasite transmission can cause parasites to favor sex rather than oppose it. In contrast to previous predictions, the model shows that weakly virulent parasites are more likely to favor sex than are highly virulent ones. Parasites have figured prominently in discussions of the evolution of sex, but recent models suggest that parasites often select against sex rather than for it. With the inclusion of small and realistic exposure biases, parasites are much more likely to favor sex. Though parasites alone may not provide a complete explanation for sex, the results presented here expand the potential for parasites to contribute to the maintenance of sex rather than act against it.

A critical approach to the definition of Darwinian units of selection.

PubMed

Rinkevich, B

2000-12-01

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.

Sexual selection and the evolution of genital shape and complexity in water striders.

PubMed

Rowe, Locke; Arnqvist, Göran

2012-01-01

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Monkeys into Men and Men into Monkeys: Chance and Contingency in the Evolution of Man, Mind and Morals in Charles Kingsley's Water Babies.

PubMed

Hale, Piers J

2013-01-01

The nineteenth century theologian, author and poet Charles Kingsley was a notable populariser of Darwinian evolution. He championed Darwin's cause and that of honesty in science for more than a decade from 1859 to 1871. Kingsley's interpretation of evolution shaped his theology, his politics and his views on race. The relationship between men and apes set the context for Kingsley's consideration of these issues. Having defended Darwin for a decade in 1871 Kingsley was dismayed to read Darwin's account of the evolution of morals in Descent of Man. He subsequently distanced himself from Darwin's conclusions even though he remained an ardent evolutionist until his death in 1875.

Models of microbiome evolution incorporating host and microbial selection.

PubMed

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

The Puzzle of HIV Neutral and Selective Evolution.

PubMed

Leitner, Thomas

2018-06-01

HIV is one of the fastest evolving organisms known. It evolves about 1 million times faster than its host, humans. Because HIV establishes chronic infections, with continuous evolution, its divergence within a single infected human surpasses the divergence of the entire humanoid history. Yet, it is still the same virus, infecting the same cell types and using the same replication machinery year after year. Hence, one would think that most mutations that HIV accumulates are neutral. But the picture is more complicated than that. HIV evolution is also a clear example of strong positive selection, that is, mutants have a survival advantage. How do these facts come together?

Origin of symbol-using systems: speech, but not sign, without the semantic urge

PubMed Central

Sereno, Martin I.

2014-01-01

Natural language—spoken and signed—is a multichannel phenomenon, involving facial and body expression, and voice and visual intonation that is often used in the service of a social urge to communicate meaning. Given that iconicity seems easier and less abstract than making arbitrary connections between sound and meaning, iconicity and gesture have often been invoked in the origin of language alongside the urge to convey meaning. To get a fresh perspective, we critically distinguish the origin of a system capable of evolution from the subsequent evolution that system becomes capable of. Human language arose on a substrate of a system already capable of Darwinian evolution; the genetically supported uniquely human ability to learn a language reflects a key contact point between Darwinian evolution and language. Though implemented in brains generated by DNA symbols coding for protein meaning, the second higher-level symbol-using system of language now operates in a world mostly decoupled from Darwinian evolutionary constraints. Examination of Darwinian evolution of vocal learning in other animals suggests that the initial fixation of a key prerequisite to language into the human genome may actually have required initially side-stepping not only iconicity, but the urge to mean itself. If sign languages came later, they would not have faced this constraint. PMID:25092671

The rule of declining adaptability in microbial evolution experiments

PubMed Central

Couce, Alejandro; Tenaillon, Olivier A.

2015-01-01

One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss these possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research. PMID:25815007

Lognormals for SETI, Evolution and Mass Extinctions

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2014-12-01

In a series of recent papers (Refs. [1-5,7,8]) and in a book (Ref. [6]), this author suggested a new mathematical theory capable of merging Darwinian Evolution and SETI into a unified statistical framework. In this new vision, Darwinian Evolution, as it unfolded on Earth over the last 3.5 billion years, is defined as just one particular realization of a certain lognormal stochastic process in the number of living species on Earth, whose mean value increased in time exponentially. SETI also may be brought into this vision since the number of communicating civilizations in the Galaxy is given by a lognormal distribution (Statistical Drake Equation). Now, in this paper we further elaborate on all that particularly with regard to two important topics: The introduction of the general lognormal stochastic process L(t) whose mean value may be an arbitrary continuous function of the time, m(t), rather than just the exponential mGBM (t) =N0eμt typical of the Geometric Brownian Motion (GBM). This is a considerable generalization of the GBM-based theory used in Refs. [1-8]. The particular application of the general stochastic process L(t) to the understanding of Mass Extinctions like the K-Pg one that marked the dinosaurs' end 65 million years ago. We first model this Mass Extinction as a decreasing Geometric Brownian Motion (GBM) extending from the asteroid's impact time all through the ensuing 'nuclear winter'. However, this model has a flaw: the 'final value' of the GBM cannot have a horizontal tangent, as requested to enable the recovery of life again after this 'final extinction value'. That flaw, however, is removed if the rapidly decreasing mean value function of L(t) is the left branch of a parabola extending from the asteroid's impact time all through the ensuing 'nuclear winter' and up to the time when the number of living species on Earth started growing up again, as we show mathematically in Section 3. In conclusion, we have uncovered an important generalization

The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

NASA Astrophysics Data System (ADS)

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-08-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem.

PubMed

Zamdborg, Leonid; Holloway, David M; Merelo, Juan J; Levchenko, Vladimir F; Spirov, Alexander V

2015-06-10

Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of "genomic parasites", such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent mutators

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem

PubMed Central

Zamdborg, Leonid; Holloway, David M.; Merelo, Juan J.; Levchenko, Vladimir F.; Spirov, Alexander V.

2015-01-01

Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of “genomic parasites”, such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent

The evolution of sexes: A specific test of the disruptive selection theory.

PubMed

da Silva, Jack

2018-01-01

The disruptive selection theory of the evolution of anisogamy posits that the evolution of a larger body or greater organismal complexity selects for a larger zygote, which in turn selects for larger gametes. This may provide the opportunity for one mating type to produce more numerous, small gametes, forcing the other mating type to produce fewer, large gametes. Predictions common to this and related theories have been partially upheld. Here, a prediction specific to the disruptive selection theory is derived from a previously published game-theoretic model that represents the most complete description of the theory. The prediction, that the ratio of macrogamete to microgamete size should be above three for anisogamous species, is supported for the volvocine algae. A fully population genetic implementation of the model, involving mutation, genetic drift, and selection, is used to verify the game-theoretic approach and accurately simulates the evolution of gamete sizes in anisogamous species. This model was extended to include a locus for gamete motility and shows that oogamy should evolve whenever there is costly motility. The classic twofold cost of sex may be derived from the fitness functions of these models, showing that this cost is ultimately due to genetic conflict.

Frameworks of reference: How (some) college students think about biological evolution

NASA Astrophysics Data System (ADS)

Filisky, Michael

1999-12-01

Evolution, a key concept for understanding all of biology, is often misunderstood by students from elementary school to graduate school. In order to teach evolution effectively, as well as to teach the biological concepts necessary for understanding evolution, teachers need to understand the initial ideas that students bring with them to the learning experience. Research has shown that many students are likely to hold alternative conceptions that may block their ability to learn evolution. The goal of this study is to contribute to the effectiveness of teaching evolution at the high school and college levels both by investigating concepts that students bring with them to their first college study of evolution, and by examining the conceptual frameworks that support these students as they construct new understanding. This study was executed in two stages. An initial survey of evolutionary understanding was administered to 203 undergraduate students in two courses at two universities in the area of Boston, MA. The surveys elicited short, written responses to five real and fictitious scenarios about biological inheritance and evolutionary change. Responses were coded into categories of concepts. The data were analyzed for patterns of understanding. Students exhibiting concepts from each of the major categories were randomly selected to participate in the subsequent interview stage of the study. Interviews with six of the students were conducted based on an interview guide employing scenarios similar to those from the survey. Analyses of the interview transcripts included the construction of detailed concept maps for each response followed by narratives of each interviewee's conceptual frameworks. The results of both stages of the study revealed a range of alternative conceptions about evolution, including scientifically acceptable Darwinian ideas and other ideas---including Lamarckian inheritance of acquired characteristics---are not accepted by modern science. The

Evolutionary psychology and evolutionary developmental psychology: understanding the evolution of human behavior and development.

PubMed

Hernández Blasi, Carlos; Causey, Kayla

2010-02-01

This is an introduction to this special issue on evolutionary psychology (EP) and evolutionary developmental psychology (EDP). We suggest here that, contrary to some common assumptions, mainstream psychology continues to be essentially non Darwinian and that EP and EDP are new approaches that can potentially help us to change this situation. We then present the organization of the special issue (composed of six papers). We conclude that evolution is certainly not the final consideration in psychology, but emphasize its importance as the basis upon which all modern behaviors and development are built.

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in

Hard and Soft Selection Revisited: How Evolution by Natural Selection Works in the Real World.

PubMed

Reznick, David

2016-01-01

The modern synthesis of evolutionary biology unified Darwin's natural selection with Mendelian genetics, but at the same time it created the dilemma of genetic load. Lewontin and Hubby's (1966) and Harris's (1966) characterization of genetic variation in natural populations increased the apparent burden of this load. Neutrality or near neutrality of genetic variation was one mechanism proposed for the revealed excessive genetic variation. Bruce Wallace coined the term "soft selection" to describe an alternative way for natural selection to operate that was consistent with observed variation. He envisioned nature as presenting ecological vacancies that could be filled by diverse genotypes. Survival and successful reproduction was a combined function of population density, genotype, and genotype frequencies, rather than a fixed value of the relative fitness of each genotype. My goal in this review is to explore the importance of soft selection in the real world. My motive and that of my colleagues as described here is not to explain what maintains genetic variation in natural populations, but rather to understand the factors that shape how organisms adapt to natural environments. We characterize how feedbacks between ecology and evolution shape both evolution and ecology. These feedbacks are mediated by density- and frequency-dependent selection, the mechanisms that underlie soft selection. Here, I report on our progress in characterizing these types of selection with a combination of a consideration of the published literature and the results from my collaborators' and my research on natural populations of guppies. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Post-Darwinian Controversies

NASA Astrophysics Data System (ADS)

Moore, James R.

1981-11-01

Preface; Introduction: the terrain of revision; Part I. Historians and Historiography: 1. Draper, White, and the military metaphor; 2. Politics, polemics, and the military milieu; 3. Warfare's toll in historical interpretation; 4. Towards a non-violent history; Part II. Darwinism and Evolutionary Thought: 5. Darwinism in transition; 6. The challenge of Lamarckian evolution; 7. The vogue of Herbert Spencer; 8. Darwinism and Neo-Darwinism; Part III. Theology and Evolution: 9. Christian anti-Darwinism: the realm of certainty and fixity; 10. Christian Darwinism: the role of providence and progress; 11. Christian Darwinism: the relevance of orthodox theology; 12. Darwinism and Darwinisticism in theology; Conclusion; Notes to the text; Bibliography; Index.

Relaxed selection is a precursor to the evolution of phenotypic plasticity.

PubMed

Hunt, Brendan G; Ometto, Lino; Wurm, Yannick; Shoemaker, DeWayne; Yi, Soojin V; Keller, Laurent; Goodisman, Michael A D

2011-09-20

Phenotypic plasticity allows organisms to produce alternative phenotypes under different conditions and represents one of the most important ways by which organisms adaptively respond to the environment. However, the relationship between phenotypic plasticity and molecular evolution remains poorly understood. We addressed this issue by investigating the evolution of genes associated with phenotypically plastic castes, sexes, and developmental stages of the fire ant Solenopsis invicta. We first determined if genes associated with phenotypic plasticity in S. invicta evolved at a rapid rate, as predicted under theoretical models. We found that genes differentially expressed between S. invicta castes, sexes, and developmental stages all exhibited elevated rates of evolution compared with ubiquitously expressed genes. We next investigated the evolutionary history of genes associated with the production of castes. Surprisingly, we found that orthologs of caste-biased genes in S. invicta and the social bee Apis mellifera evolved rapidly in lineages without castes. Thus, in contrast to some theoretical predictions, our results suggest that rapid rates of molecular evolution may not arise primarily as a consequence of phenotypic plasticity. Instead, genes evolving under relaxed purifying selection may more readily adopt new forms of biased expression during the evolution of alternate phenotypes. These results suggest that relaxed selective constraint on protein-coding genes is an important and underappreciated element in the evolutionary origin of phenotypic plasticity.

Evolution of Students' Ideas about Natural Selection through a Constructivist Framework

ERIC Educational Resources Information Center

Baumgartner, Erin; Duncan, Kanesa

2009-01-01

Educating students about the process of evolution through natural selection is vitally important because not only is it the unifying theory of biological science, it is also widely regarded as difficult for students to fully comprehend. Anderson and colleagues (2002) describe alternative ideas and misconceptions about natural selection as highly…

Sperm Bindin Divergence under Sexual Selection and Concerted Evolution in Sea Stars.

PubMed

Patiño, Susana; Keever, Carson C; Sunday, Jennifer M; Popovic, Iva; Byrne, Maria; Hart, Michael W

2016-08-01

Selection associated with competition among males or sexual conflict between mates can create positive selection for high rates of molecular evolution of gamete recognition genes and lead to reproductive isolation between species. We analyzed coding sequence and repetitive domain variation in the gene encoding the sperm acrosomal protein bindin in 13 diverse sea star species. We found that bindin has a conserved coding sequence domain structure in all 13 species, with several repeated motifs in a large central region that is similar among all sea stars in organization but highly divergent among genera in nucleotide and predicted amino acid sequence. More bindin codons and lineages showed positive selection for high relative rates of amino acid substitution in genera with gonochoric outcrossing adults (and greater expected strength of sexual selection) than in selfing hermaphrodites. That difference is consistent with the expectation that selfing (a highly derived mating system) may moderate the strength of sexual selection and limit the accumulation of bindin amino acid differences. The results implicate both positive selection on single codons and concerted evolution within the repetitive region in bindin divergence, and suggest that both single amino acid differences and repeat differences may affect sperm-egg binding and reproductive compatibility. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Teaching Evolution: A Heuristic Study of Personal and Cultural Dissonance

NASA Astrophysics Data System (ADS)

Grimes, Larry G.

Darwinian evolution is a robustly supported scientific theory. Yet creationists continue to challenge its teaching in American public schools. Biology teachers in all 50 states are responsible for teaching science content standards that include evolution. As products of their backgrounds and affiliations teachers bring personal attitudes and beliefs to their teaching. The purpose of this study was to explore how biology teachers perceive, describe, and value their teaching of evolution. This research question was explored through a heuristic qualitative methodology. Eight veteran California high school biology teachers were queried as to their beliefs, perceptions, experiences and practices of teaching evolution. Both personal and professional documents were collected. Data was presented in the form of biographical essays that highlight teachers' backgrounds, experiences, perspectives and practices of teaching evolution. Of special interest was how they describe pressure over teaching evolution during a decade of standards and No Child Left Behind high-stakes testing mandates. Five common themes emerged. Standards have increased the overall amount of evolution that is taught. High-stakes testing has decreased the depth at which evolution is taught. Teacher belief systems strongly influence how evolution is taught. Fear of creationist challenges effect evolution teaching strategies. And lastly, concern over the potential effects of teaching evolution on student worldviews was mixed. Three categories of teacher concern over the potential impact of evolution on student worldviews were identified: Concerned, Strategist, and Carefree. In the final analysis teacher beliefs and attitudes still appeared to he the most important factor influencing how evolution is taught.

Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.

PubMed

Edwards, C T T; Holmes, E C; Pybus, O G; Wilson, D J; Viscidi, R P; Abrams, E J; Phillips, R E; Drummond, A J

2006-11-01

The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic diversity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences sampled longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.

Science for Survival: The Modern Synthesis of Evolution and The Biological Sciences Curriculum Study

NASA Astrophysics Data System (ADS)

Green, Lisa Anne

In this historical dissertation, I examined the process of curriculum development in the Biological Sciences Curriculum Study (BSCS) in the United States during the period 1959-1963. The presentation of evolution in the high school texts was based on a more robust form of Darwinian evolution which developed during the 1930s and 1940s called "the modern synthesis of evolution." Building primarily on the work of historians Vassiliki Smocovitis and John L. Rudolph, I used the archival papers and published writings of the four architects of the modern synthesis and the four most influential leaders of the BSCS in regards to evolution to investigate how the modern synthetic theory of evolution shaped the BSCS curriculum. The central question was "Why was evolution so important to the BSCS to make it the central theme of the texts?" Important answers to this question had already been offered in the historiography, but it was still not clear why every citizen in the world needed to understand evolution. I found that the emphasis on natural selection in the modern synthesis shifted the focus away from humans as passive participants to the recognition that humans are active agents in their own cultural and biological evolution. This required re-education of the world citizenry, which was accomplished in part by the BSCS textbooks. I also found that BSCS leaders Grobman, Glass, and Muller had serious concerns regarding the effects of nuclear radiation on the human gene pool, and were actively involved in informing th public. Lastly, I found that concerns of 1950s reform eugenicists were addressed in the BSCS textbooks, without mentioning eugenics by name. I suggest that the leaders of the BSCS, especially Bentley Glass and Hermann J. Muller, thought that students needed to understand genetics and evolution to be able to make some of the tough choices they might be called on to make as the dominant species on earth and the next reproductive generation in the nuclear age. This

Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

PubMed

Pallen, M J; Gophna, U

2007-01-01

Bacterial flagella at first sight appear uniquely sophisticated in structure, so much so that they have even been considered 'irreducibly complex' by the intelligent design movement. However, a more detailed analysis reveals that these remarkable pieces of molecular machinery are the product of processes that are fully compatible with Darwinian evolution. In this chapter we present evidence for such processes, based on a review of experimental studies, molecular phylogeny and microbial genomics. Several processes have played important roles in flagellar evolution: self-assembly of simple repeating subunits, gene duplication with subsequent divergence, recruitment of elements from other systems ('molecular bricolage'), and recombination. We also discuss additional tentative new assignments of homology (FliG with MgtE, FliO with YscJ). In conclusion, rather than providing evidence of intelligent design, flagellar and non-flagellar Type III secretion systems instead provide excellent case studies in the evolution of complex systems from simpler components.

Tuning Spatial Profiles of Selection Pressure to Modulate the Evolution of Drug Resistance

NASA Astrophysics Data System (ADS)

De Jong, Maxwell G.; Wood, Kevin B.

2018-06-01

Spatial heterogeneity plays an important role in the evolution of drug resistance. While recent studies have indicated that spatial gradients of selection pressure can accelerate resistance evolution, much less is known about evolution in more complex spatial profiles. Here we use a stochastic toy model of drug resistance to investigate how different spatial profiles of selection pressure impact the time to fixation of a resistant allele. Using mean first passage time calculations, we show that spatial heterogeneity accelerates resistance evolution when the rate of spatial migration is sufficiently large relative to mutation but slows fixation for small migration rates. Interestingly, there exists an intermediate regime—characterized by comparable rates of migration and mutation—in which the rate of fixation can be either accelerated or decelerated depending on the spatial profile, even when spatially averaged selection pressure remains constant. Finally, we demonstrate that optimal tuning of the spatial profile can dramatically slow the spread and fixation of resistant subpopulations, even in the absence of a fitness cost for resistance. Our results may lay the groundwork for optimized, spatially resolved drug dosing strategies for mitigating the effects of drug resistance.

Experimental evolution in Drosophila melanogaster: interaction of temperature and food quality selection regimes.

PubMed

Bochdanovits, Zoltán; de Jong, Gerdien

2003-08-01

In Drosophila, both the phenotypic and evolutionary effect of temperature on adult size involves alterations to larval resource processing and affects other life-history traits, that is, development time but most notably, larval survival. Therefore, thermal evolution of adult body size might not be independent of simultaneous adaptation of larval traits to resource availability. Using experimental evolution lines adapted to high and low temperatures at different levels of food, we show that selection pressures interact in shaping larval resource processing. Evolution on poor food invariably leads to lower resource acquisition suggesting a cost to feeding behavior. However, following low temperature selection, lower resource acquisition led to a higher adult body size, probably by more efficient allocation to growth. In contrast, following high temperature selection, low resource acquisition benefited larval survival, possibly by reducing feeding-associated costs. We show that evolved differences to larval resource processing provide a possible proximate mechanism to variation in a suite of correlated life-history traits during adaptation to different climates. The implication for natural populations is that in nature, thermal evolution drives populations to opposite ends of an adult size versus larval survival trade-off by altering resource processing, if resource availability is limited.

The importance of selection in the evolution of blindness in cavefish.

PubMed

Cartwright, Reed A; Schwartz, Rachel S; Merry, Alexandra L; Howell, Megan M

2017-02-07

Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. We estimate that the selection coefficient for blindness would need to be at least 0.005 (and maybe as high as 0.5) for blindness to evolve in the model cave-organism, Astyanax mexicanus. Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development.

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds

PubMed Central

Dean, Rebecca; Harrison, Peter W.; Wright, Alison E.; Zimmer, Fabian; Mank, Judith E.

2015-01-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. PMID:26067773

Anthropogenic selection enhances cancer evolution in Tasmanian devil tumours.

PubMed

Ujvari, Beata; Pearse, Anne-Maree; Swift, Kate; Hodson, Pamela; Hua, Bobby; Pyecroft, Stephen; Taylor, Robyn; Hamede, Rodrigo; Jones, Menna; Belov, Katherine; Madsen, Thomas

2014-02-01

The Tasmanian Devil Facial Tumour Disease (DFTD) provides a unique opportunity to elucidate the long-term effects of natural and anthropogenic selection on cancer evolution. Since first observed in 1996, this transmissible cancer has caused local population declines by >90%. So far, four chromosomal DFTD variants (strains) have been described and karyotypic analyses of 253 tumours showed higher levels of tetraploidy in the oldest strain. We propose that increased ploidy in the oldest strain may have evolved in response to effects of genomic decay observed in asexually reproducing organisms. In this study, we focus on the evolutionary response of DFTD to a disease suppression trial. Tumours collected from devils subjected to the removal programme showed accelerated temporal evolution of tetraploidy compared with tumours from other populations where no increase in tetraploid tumours were observed. As ploidy significantly reduces tumour growth rate, we suggest that the disease suppression trial resulted in selection favouring slower growing tumours mediated by an increased level of tetraploidy. Our study reveals that DFTD has the capacity to rapidly respond to novel selective regimes and that disease eradication may result in novel tumour adaptations, which may further imperil the long-term survival of the world's largest carnivorous marsupial.

Anthropogenic selection enhances cancer evolution in Tasmanian devil tumours

PubMed Central

Ujvari, Beata; Pearse, Anne-Maree; Swift, Kate; Hodson, Pamela; Hua, Bobby; Pyecroft, Stephen; Taylor, Robyn; Hamede, Rodrigo; Jones, Menna; Belov, Katherine; Madsen, Thomas

2014-01-01

The Tasmanian Devil Facial Tumour Disease (DFTD) provides a unique opportunity to elucidate the long-term effects of natural and anthropogenic selection on cancer evolution. Since first observed in 1996, this transmissible cancer has caused local population declines by >90%. So far, four chromosomal DFTD variants (strains) have been described and karyotypic analyses of 253 tumours showed higher levels of tetraploidy in the oldest strain. We propose that increased ploidy in the oldest strain may have evolved in response to effects of genomic decay observed in asexually reproducing organisms. In this study, we focus on the evolutionary response of DFTD to a disease suppression trial. Tumours collected from devils subjected to the removal programme showed accelerated temporal evolution of tetraploidy compared with tumours from other populations where no increase in tetraploid tumours were observed. As ploidy significantly reduces tumour growth rate, we suggest that the disease suppression trial resulted in selection favouring slower growing tumours mediated by an increased level of tetraploidy. Our study reveals that DFTD has the capacity to rapidly respond to novel selective regimes and that disease eradication may result in novel tumour adaptations, which may further imperil the long-term survival of the world's largest carnivorous marsupial. PMID:24567746

Selection for Social Signalling Drives the Evolution of Chameleon Colour Change

PubMed Central

Stuart-Fox, Devi; Moussalli, Adnan

2008-01-01

Rapid colour change is a remarkable natural phenomenon that has evolved in several vertebrate and invertebrate lineages. The two principal explanations for the evolution of this adaptive strategy are (1) natural selection for crypsis (camouflage) against a range of different backgrounds and (2) selection for conspicuous social signals that maximise detectability to conspecifics, yet minimise exposure to predators because they are only briefly displayed. Here we show that evolutionary shifts in capacity for colour change in southern African dwarf chameleons (Bradypodion spp.) are associated with increasingly conspicuous signals used in male contests and courtship. To the chameleon visual system, species showing the most dramatic colour change display social signals that contrast most against the environmental background and amongst adjacent body regions. We found no evidence for the crypsis hypothesis, a finding reinforced by visual models of how both chameleons and their avian predators perceive chameleon colour variation. Instead, our results suggest that selection for conspicuous social signals drives the evolution of colour change in this system, supporting the view that transitory display traits should be under strong selection for signal detectability. PMID:18232740

A conceptual framework for the evolutionary origins of multicellularity

NASA Astrophysics Data System (ADS)

Libby, Eric; Rainey, Paul B.

2013-06-01

The evolution of multicellular organisms from unicellular counterparts involved a transition in Darwinian individuality from single cells to groups. A particular challenge is to understand the nature of the earliest groups, the causes of their evolution, and the opportunities for emergence of Darwinian properties. Here we outline a conceptual framework based on a logical set of possible pathways for evolution of the simplest self-replicating groups. Central to these pathways is the recognition of a finite number of routes by which genetic information can be transmitted between individual cells and groups. We describe the form and organization of each primordial group state and consider factors affecting persistence and evolution of the nascent multicellular forms. Implications arising from our conceptual framework become apparent when attempting to partition fitness effects at individual and group levels. These are discussed with reference to the evolutionary emergence of individuality and its manifestation in extant multicellular life—including those of marginal Darwinian status.

Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution.

PubMed

Wright, Alison E; Harrison, Peter W; Zimmer, Fabian; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

2015-03-01

Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster-Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster-Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution. © 2015 John Wiley & Sons Ltd.

The (De-)Evolution of Evolution Games: A Content Analysis of the Representation of Evolution through Natural Selection in Digital Games

ERIC Educational Resources Information Center

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-01-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a…

Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

PubMed

Voloch, Carolina M; Capellão, Renata T; Mello, Beatriz; Schrago, Carlos G

2014-11-19

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

PubMed Central

Voloch, Carolina M.; Capellão, Renata T.; Mello, Beatriz; Schrago, Carlos G.

2014-01-01

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups. PMID:25415197

Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea).

PubMed

Yang, Ji; Gu, Hongya; Yang, Ziheng

2004-01-01

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A-E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (omega = d(N)/ d(S)) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.

A step towards ending the isolation of behavior analysis: A common language with evolutionary science

PubMed Central

Brown, J. F.; Hendy, Steve

2001-01-01

In spite of repeated efforts to explain itself to a wider audience, behavior analysis remains a largely misunderstood and isolated discipline. In this article we argue that this situation is in part due to the terms we use in our technical discussions. In particular, reinforcement and punishment, with their vernacular associations of reward and retribution, are a source of much misunderstanding. Although contemporary thinking within behavior analysis holds that reinforcement and punishment are Darwinian processes whereby behavioral variants are selected and deselected by their consequences, the continued use of the terms reinforcement and punishment to account for behavioral evolution obscures this fact. To clarify and simplify matters, we propose replacing the terms reinforcement and punishment with selection and deselection, respectively. These changes would provide a terminological meeting point with other selectionist sciences, thereby increasing the likelihood that behavior analysis will contribute to Darwinian science. PMID:22478361

Quantitative Clinical Imaging Methods for Monitoring Intratumoral Evolution.

PubMed

Kim, Joo Yeun; Gatenby, Robert A

2017-01-01

regional dynamics so that the internal diversity of tumors is the net result of complex multiscale somatic Darwinian interactions.Methods in landscape ecology harness Darwinian dynamics to link the environmental properties of a given region to the local populations which are assumed to represent maximally fit phenotypes within those conditions. Consider a common task of a landscape ecologist: defining the spatial distribution of species in a large region, e.g., in a satellite image. Clearly the most accurate approach requires a meter by meter survey of the multiple square kilometers in the region of interest. However, this is both impractical and potentially destructive. Instead, landscape ecology breaks the task into component parts relying on the Darwinian interdependence of environmental properties and fitness of specific species' phenotypic and genotypic properties. First, the satellite map is carefully analyzed to define the number and distribution of habitats. Then the species distribution in a representative sampling of each habitat is empirically determined. Ultimately, this permits sufficient bridging of spatial scales to accurately predict spatial distribution of plant and animal species within large regions.Currently, identifying intratumoral subpopulations requires detailed histological and molecular studies that are expensive and time consuming. Furthermore, this method is subject to sampling bias, is invasive for vital organs such as the brain, and inherently destructive precluding repeated assessments for monitoring post-treatment response and proteogenomic evolution. In contrast, modern cross-sectional imaging can interrogate the entire tumor noninvasively, allowing repeated analysis without disrupting the region of interest. In particular, magnetic resonance imaging (MRI) provides exceptional spatial resolution and generates signals that are unique to the molecular constituents of tissue. Here we propose that MRI scans may be the equivalent of satellite

Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes

PubMed Central

Mitterboeck, T. Fatima; Liu, Shanlin; Adamowicz, Sarah J.; Fu, Jinzhong; Zhang, Rui; Song, Wenhui; Meusemann, Karen

2017-01-01

Abstract The evolution of powered flight is a major innovation that has facilitated the success of insects. Previously, studies of birds, bats, and insects have detected molecular signatures of differing selection regimes in energy-related genes associated with flight evolution and/or loss. Here, using DNA sequences from more than 1000 nuclear and mitochondrial protein-coding genes obtained from insect transcriptomes, we conduct a broader exploration of which gene categories display positive and relaxed selection at the origin of flight as well as with multiple independent losses of flight. We detected a number of categories of nuclear genes more often under positive selection in the lineage leading to the winged insects (Pterygota), related to catabolic processes such as proteases, as well as splicing-related genes. Flight loss was associated with relaxed selection signatures in splicing genes, mirroring the results for flight evolution. Similar to previous studies of flight loss in various animal taxa, we observed consistently higher nonsynonymous-to-synonymous substitution ratios in mitochondrial genes of flightless lineages, indicative of relaxed selection in energy-related genes. While oxidative phosphorylation genes were not detected as being under selection with the origin of flight specifically, they were most often detected as being under positive selection in holometabolous (complete metamorphosis) insects as compared with other insect lineages. This study supports some convergence in gene-specific selection pressures associated with flight ability, and the exploratory analysis provided some new insights into gene categories potentially associated with the gain and loss of flight in insects. PMID:29020740

Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes.

PubMed

Mitterboeck, T Fatima; Liu, Shanlin; Adamowicz, Sarah J; Fu, Jinzhong; Zhang, Rui; Song, Wenhui; Meusemann, Karen; Zhou, Xin

2017-10-01

The evolution of powered flight is a major innovation that has facilitated the success of insects. Previously, studies of birds, bats, and insects have detected molecular signatures of differing selection regimes in energy-related genes associated with flight evolution and/or loss. Here, using DNA sequences from more than 1000 nuclear and mitochondrial protein-coding genes obtained from insect transcriptomes, we conduct a broader exploration of which gene categories display positive and relaxed selection at the origin of flight as well as with multiple independent losses of flight. We detected a number of categories of nuclear genes more often under positive selection in the lineage leading to the winged insects (Pterygota), related to catabolic processes such as proteases, as well as splicing-related genes. Flight loss was associated with relaxed selection signatures in splicing genes, mirroring the results for flight evolution. Similar to previous studies of flight loss in various animal taxa, we observed consistently higher nonsynonymous-to-synonymous substitution ratios in mitochondrial genes of flightless lineages, indicative of relaxed selection in energy-related genes. While oxidative phosphorylation genes were not detected as being under selection with the origin of flight specifically, they were most often detected as being under positive selection in holometabolous (complete metamorphosis) insects as compared with other insect lineages. This study supports some convergence in gene-specific selection pressures associated with flight ability, and the exploratory analysis provided some new insights into gene categories potentially associated with the gain and loss of flight in insects. © The Authors 2017. Published by Oxford University Press.

Experimental evolution of a sexually selected display in yeast

PubMed Central

Rogers, David W.; Greig, Duncan

2008-01-01

The fundamental principle underlying sexual selection theory is that an allele conferring an advantage in the competition for mates will spread through a population. Remarkably, this has never been demonstrated empirically. We have developed an experimental system using yeast for testing genetic models of sexual selection. Yeast signal to potential partners by producing an attractive pheromone; stronger signallers are preferred as mates. We tested the effect of high and low levels of sexual selection on the evolution of a gene determining the strength of this signal. Under high sexual selection, an allele encoding a stronger signal was able to invade a population of weak signallers, and we observed a corresponding increase in the amount of pheromone produced. By contrast, the strong signalling allele failed to invade under low sexual selection. Our results demonstrate, for the first time, the spread of a sexually selected allele through a population, confirming the central assumption of sexual selection theory. Our yeast system is a powerful tool for investigating the genetics of sexual selection. PMID:18842545

The role of weak selection and high mutation rates in nearly neutral evolution.

PubMed

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2009-04-21

Neutral dynamics occur in evolution if all types are 'effectively equal' in their reproductive success, where the definition of 'effectively equal' depends on the population size and the details of mutations. Empirically observed neutral genetic evolution in extremely large clonal populations can only be explained under current models if selection is completely absent. Such models typically consider the case where population dynamics occurs on a different timescale to evolution. However, this assumption is invalid when mutations are not rare in a whole population. We show that this has important consequences for the occurrence of neutral evolution in clonal populations. In highly connected type spaces, neutral dynamics can occur for all population sizes despite significant selective differences, via the forming of effectively neutral networks connecting rare neutral types. Biological implications include an explanation for the high diversity of rare types that survive in large clonal populations, and a theoretical justification for the use of neutral null models.

Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today

NASA Astrophysics Data System (ADS)

Kutschera, Ulrich

2009-11-01

The book On the Origin of Species, published in November 1859, is an “abstract” without references, compiled by Charles Darwin from a much longer manuscript entitled “Natural Selection.” Here, I summarize the five theories that can be extracted from Darwin’s monograph, explain the true meaning of the phrase “struggle for life” (i.e., competition and cooperation), and outline Darwin’s original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that “selection only eliminates but is not creative” is still alive today. However, I document that August Weismann ( Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen ( Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this “Weismann-Schmalhausen principle” with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky ( Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by

Antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in Drosophila simulans.

PubMed

Sharma, Manmohan D; Hunt, John; Hosken, David J

2012-03-01

Natural and sexual selection are classically thought to oppose one another, and although there is evidence for this, direct experimental demonstrations of this antagonism are largely lacking. Here, we assessed the effects of sexual and natural selection on the evolution of cuticular hydrocarbons (CHCs), a character subject to both modes of selection, in Drosophila simulans. Natural selection and sexual selection were manipulated in a fully factorial design, and after 27 generations of experimental evolution, the responses of male and female CHCs were assessed. The effects of natural and sexual selection differed greatly across the sexes. The responses of female CHCs were generally small, but CHCs evolved predominantly in the direction of natural selection. For males, profiles evolved via sexual and natural selection, as well as through the interaction between the two, with some male CHC components only evolving in the direction of natural selection when sexual selection was relaxed. These results indicate sex-specific responses to selection, and that sexual and natural selection act antagonistically for at least some combinations of CHCs. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Colder environments did not select for a faster metabolism during experimental evolution of Drosophila melanogaster.

PubMed

Alton, Lesley A; Condon, Catriona; White, Craig R; Angilletta, Michael J

2017-01-01

The effect of temperature on the evolution of metabolism has been the subject of debate for a century; however, no consistent patterns have emerged from comparisons of metabolic rate within and among species living at different temperatures. We used experimental evolution to determine how metabolism evolves in populations of Drosophila melanogaster exposed to one of three selective treatments: a constant 16°C, a constant 25°C, or temporal fluctuations between 16 and 25°C. We tested August Krogh's controversial hypothesis that colder environments select for a faster metabolism. Given that colder environments also experience greater seasonality, we also tested the hypothesis that temporal variation in temperature may be the factor that selects for a faster metabolism. We measured the metabolic rate of flies from each selective treatment at 16, 20.5, and 25°C. Although metabolism was faster at higher temperatures, flies from the selective treatments had similar metabolic rates at each measurement temperature. Based on variation among genotypes within populations, heritable variation in metabolism was likely sufficient for adaptation to occur. We conclude that colder or seasonal environments do not necessarily select for a faster metabolism. Rather, other factors besides temperature likely contribute to patterns of metabolic rate over thermal clines in nature. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

The evolution of female ornaments and weaponry: social selection, sexual selection and ecological competition.

PubMed

Tobias, Joseph A; Montgomerie, Robert; Lyon, Bruce E

2012-08-19

Ornaments, weapons and aggressive behaviours may evolve in female animals by mate choice and intrasexual competition for mating opportunities-the standard forms of sexual selection in males. However, a growing body of evidence suggests that selection tends to operate in different ways in males and females, with female traits more often mediating competition for ecological resources, rather than mate acquisition. Two main solutions have been proposed to accommodate this disparity. One is to expand the concept of sexual selection to include all mechanisms related to fecundity; another is to adopt an alternative conceptual framework-the theory of social selection-in which sexual selection is one component of a more general form of selection resulting from all social interactions. In this study, we summarize the history of the debate about female ornaments and weapons, and discuss potential resolutions. We review the components of fitness driving ornamentation in a wide range of systems, and show that selection often falls outside the limits of traditional sexual selection theory, particularly in females. We conclude that the evolution of these traits in both sexes is best understood within the unifying framework of social selection.

Selection platforms for directed evolution in synthetic biology

PubMed Central

Tizei, Pedro A.G.; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B.

2016-01-01

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules–gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function–be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. PMID:27528765

Hominid evolution: genetics versus memetics

NASA Astrophysics Data System (ADS)

Carter, Brandon

2012-01-01

The last few million years on planet Earth have witnessed two remarkable phases of hominid development, starting with a phase of biological evolution characterized by rather rapid increase of the size of the brain. This has been followed by a phase of even more rapid technological evolution and concomitant expansion of the size of the population that began when our own particular ‘sapiens’ species emerged, just a few hundred thousand years ago. The present investigation exploits the analogy between the neo-Darwinian genetic evolution mechanism governing the first phase, and the memetic evolution mechanism governing the second phase. From the outset of the latter until very recently - about the year 2000 - the growth of the global population N was roughly governed by an equation of the form dN/Ndt=N/T*, in which T* is a coefficient introduced (in 1960) by von Foerster, who evaluated it empirically as about 200 000 million years. It is shown here how the value of this hitherto mysterious timescale governing the memetic phase is explicable in terms of what happened in the preceding genetic phase. The outcome is that the order of magnitude of the Foerster timescale can be accounted for as the product of the relevant (human) generation timescale, about 20 years, with the number of bits of information in the genome, of the order of 10 000 million. Whereas the origin of our ‘homo’ genus may well have involved an evolutionary hard step, it transpires that the emergence of our particular ‘sapiens’ species was rather an automatic process.

Rapid evolution and copy number variation of primate RHOXF2, an X-linked homeobox gene involved in male reproduction and possibly brain function.

PubMed

Niu, Ao-lei; Wang, Yin-qiu; Zhang, Hui; Liao, Cheng-hong; Wang, Jin-kai; Zhang, Rui; Che, Jun; Su, Bing

2011-10-12

Darwinian positive selection acting on the male reproductive system and possibly also on the central nervous system, which sheds light on understanding the role of homeobox genes in adaptive evolution.

Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of Mitochondria

PubMed Central

Christie, Joshua R.; Schaerf, Timothy M.; Beekman, Madeleine

2015-01-01

Why are mitochondria almost always inherited from one parent during sexual reproduction? Current explanations for this evolutionary mystery include conflict avoidance between the nuclear and mitochondrial genomes, clearing of deleterious mutations, and optimization of mitochondrial-nuclear coadaptation. Mathematical models, however, fail to show that uniparental inheritance can replace biparental inheritance under any existing hypothesis. Recent empirical evidence indicates that mixing two different but normal mitochondrial haplotypes within a cell (heteroplasmy) can cause cell and organism dysfunction. Using a mathematical model, we test if selection against heteroplasmy can lead to the evolution of uniparental inheritance. When we assume selection against heteroplasmy and mutations are neither advantageous nor deleterious (neutral mutations), uniparental inheritance replaces biparental inheritance for all tested parameter values. When heteroplasmy involves mutations that are advantageous or deleterious (non-neutral mutations), uniparental inheritance can still replace biparental inheritance. We show that uniparental inheritance can evolve with or without pre-existing mating types. Finally, we show that selection against heteroplasmy can explain why some organisms deviate from strict uniparental inheritance. Thus, we suggest that selection against heteroplasmy explains the evolution of uniparental inheritance. PMID:25880558

The evolution of female ornaments and weaponry: social selection, sexual selection and ecological competition

PubMed Central

Tobias, Joseph A.; Montgomerie, Robert; Lyon, Bruce E.

2012-01-01

Ornaments, weapons and aggressive behaviours may evolve in female animals by mate choice and intrasexual competition for mating opportunities—the standard forms of sexual selection in males. However, a growing body of evidence suggests that selection tends to operate in different ways in males and females, with female traits more often mediating competition for ecological resources, rather than mate acquisition. Two main solutions have been proposed to accommodate this disparity. One is to expand the concept of sexual selection to include all mechanisms related to fecundity; another is to adopt an alternative conceptual framework—the theory of social selection—in which sexual selection is one component of a more general form of selection resulting from all social interactions. In this study, we summarize the history of the debate about female ornaments and weapons, and discuss potential resolutions. We review the components of fitness driving ornamentation in a wide range of systems, and show that selection often falls outside the limits of traditional sexual selection theory, particularly in females. We conclude that the evolution of these traits in both sexes is best understood within the unifying framework of social selection. PMID:22777016

Sexual selection accelerates signal evolution during speciation in birds.

PubMed

Seddon, Nathalie; Botero, Carlos A; Tobias, Joseph A; Dunn, Peter O; Macgregor, Hannah E A; Rubenstein, Dustin R; Uy, J Albert C; Weir, Jason T; Whittingham, Linda A; Safran, Rebecca J

2013-09-07

Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male-male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation.

Long-term dynamics of adaptive evolution in a globally important phytoplankton species to ocean acidification

PubMed Central

Schlüter, Lothar; Lohbeck, Kai T.; Gröger, Joachim P.; Riebesell, Ulf; Reusch, Thorsten B. H.

2016-01-01

Marine phytoplankton may adapt to ocean change, such as acidification or warming, because of their large population sizes and short generation times. Long-term adaptation to novel environments is a dynamic process, and phenotypic change can take place thousands of generations after exposure to novel conditions. We conducted a long-term evolution experiment (4 years = 2100 generations), starting with a single clone of the abundant and widespread coccolithophore Emiliania huxleyi exposed to three different CO2 levels simulating ocean acidification (OA). Growth rates as a proxy for Darwinian fitness increased only moderately under both levels of OA [+3.4% and +4.8%, respectively, at 1100 and 2200 μatm partial pressure of CO2 (Pco2)] relative to control treatments (ambient CO2, 400 μatm). Long-term adaptation to OA was complex, and initial phenotypic responses of ecologically important traits were later reverted. The biogeochemically important trait of calcification, in particular, that had initially been restored within the first year of evolution was later reduced to levels lower than the performance of nonadapted populations under OA. Calcification was not constitutively lost but returned to control treatment levels when high CO2–adapted isolates were transferred back to present-day control CO2 conditions. Selection under elevated CO2 exacerbated a general decrease of cell sizes under long-term laboratory evolution. Our results show that phytoplankton may evolve complex phenotypic plasticity that can affect biogeochemically important traits, such as calcification. Adaptive evolution may play out over longer time scales (>1 year) in an unforeseen way under future ocean conditions that cannot be predicted from initial adaptation responses. PMID:27419227

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.

PubMed

Shapiro, James A

2016-06-08

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

PubMed Central

Shapiro, James A.

2016-01-01

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. PMID:27338490

Human-induced evolution caused by unnatural selection through harvest of wild animals

PubMed Central

Allendorf, Fred W.; Hard, Jeffrey J.

2009-01-01

Human harvest of phenotypically desirable animals from wild populations imposes selection that can reduce the frequencies of those desirable phenotypes. Hunting and fishing contrast with agricultural and aquacultural practices in which the most desirable animals are typically bred with the specific goal of increasing the frequency of desirable phenotypes. We consider the potential effects of harvest on the genetics and sustainability of wild populations. We also consider how harvesting could affect the mating system and thereby modify sexual selection in a way that might affect recruitment. Determining whether phenotypic changes in harvested populations are due to evolution, rather than phenotypic plasticity or environmental variation, has been problematic. Nevertheless, it is likely that some undesirable changes observed over time in exploited populations (e.g., reduced body size, earlier sexual maturity, reduced antler size, etc.) are due to selection against desirable phenotypes—a process we call “unnatural” selection. Evolution brought about by human harvest might greatly increase the time required for over-harvested populations to recover once harvest is curtailed because harvesting often creates strong selection differentials, whereas curtailing harvest will often result in less intense selection in the opposing direction. We strongly encourage those responsible for managing harvested wild populations to take into account possible selective effects of harvest management and to implement monitoring programs to detect exploitation-induced selection before it seriously impacts viability. PMID:19528656

The enigma of Darwin.

PubMed

De Vries, A

1984-01-01

Darwin's theory of evolution by natural selection on the basis of inherited random individual variation and excessive offspring remains controversial. Arguments derive from religion (creationism)--disagreement with the Darwinian reduction of teleology to physical causation, from science--nonselective mechanism, and from logic--negation of the possibility of proof of any scientific theory allowing only for validity thusfar. Experimentation on Darwinism is beset with a practical obstacle--unattainable duration, and a logical one--nonpredictability inherent in the randomness of variation. Evolution and creationism need not be contradictive if viewed in their separate domains--rational versus miraculous.

Contributions of natural and sexual selection to the evolution of premating reproductive isolation: a research agenda.

PubMed

Safran, Rebecca J; Scordato, Elizabeth S C; Symes, Laurel B; Rodríguez, Rafael L; Mendelson, Tamra C

2013-11-01

Speciation by divergent natural selection is well supported. However, the role of sexual selection in speciation is less well understood due to disagreement about whether sexual selection is a mechanism of evolution separate from natural selection, as well as confusion about various models and tests of sexual selection. Here, we outline how sexual selection and natural selection are different mechanisms of evolutionary change, and suggest that this distinction is critical when analyzing the role of sexual selection in speciation. Furthermore, we clarify models of sexual selection with respect to their interaction with ecology and natural selection. In doing so, we outline a research agenda for testing hypotheses about the relative significance of divergent sexual and natural selection in the evolution of reproductive isolation. Copyright © 2013 Elsevier Ltd. All rights reserved.

FOXP2 Targets Show Evidence of Positive Selection in European Populations

PubMed Central

Ayub, Qasim; Yngvadottir, Bryndis; Chen, Yuan; Xue, Yali; Hu, Min; Vernes, Sonja C.; Fisher, Simon E.; Tyler-Smith, Chris

2013-01-01

Forkhead box P2 (FOXP2) is a highly conserved transcription factor that has been implicated in human speech and language disorders and plays important roles in the plasticity of the developing brain. The pattern of nucleotide polymorphisms in FOXP2 in modern populations suggests that it has been the target of positive (Darwinian) selection during recent human evolution. In our study, we searched for evidence of selection that might have followed FOXP2 adaptations in modern humans. We examined whether or not putative FOXP2 targets identified by chromatin-immunoprecipitation genomic screening show evidence of positive selection. We developed an algorithm that, for any given gene list, systematically generates matched lists of control genes from the Ensembl database, collates summary statistics for three frequency-spectrum-based neutrality tests from the low-coverage resequencing data of the 1000 Genomes Project, and determines whether these statistics are significantly different between the given gene targets and the set of controls. Overall, there was strong evidence of selection of FOXP2 targets in Europeans, but not in the Han Chinese, Japanese, or Yoruba populations. Significant outliers included several genes linked to cellular movement, reproduction, development, and immune cell trafficking, and 13 of these constituted a significant network associated with cardiac arteriopathy. Strong signals of selection were observed for CNTNAP2 and RBFOX1, key neurally expressed genes that have been consistently identified as direct FOXP2 targets in multiple studies and that have themselves been associated with neurodevelopmental disorders involving language dysfunction. PMID:23602712

Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies.

PubMed

Rousselle, Marjolaine; Faivre, Nicolas; Ballenghien, Marion; Galtier, Nicolas; Nabholz, Benoit

2016-10-23

The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the "fast-X" or "fast-Z" effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Continuous In Vitro Evolution of a Ribozyme that Catalyzes Three Successive Nucleotidyl Addition Reactions

NASA Technical Reports Server (NTRS)

McGinness, Kathleen E.; Wright, Martin C.; Joyce, Gerald F.

2002-01-01

Variants of the class I ligase ribozyme, which catalyzes joining of the 3' end of a template bound oligonucleotide to its own 5' end, have been made to evolve in a continuous manner by a simple serial transfer procedure that can be carried out indefinitely. This process was expanded to allow the evolution of ribozymes that catalyze three successive nucleotidyl addition reactions, two template-directed mononucleotide additions followed by RNA ligation. During the development of this behavior, a population of ribozymes was maintained against an overall dilution of more than 10(exp 406). The resulting ribozymes were capable of catalyzing the three-step reaction pathway, with nucleotide addition occurring in either a 5' yieldig 3' or a 3' yielding 5' direction. This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution.

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Sexual selection and the adaptive evolution of PKDREJ protein in primates and rodents

PubMed Central

Vicens, Alberto; Gómez Montoto, Laura; Couso-Ferrer, Francisco; Sutton, Keith A.; Roldan, Eduardo R.S.

2015-01-01

PKDREJ is a testis-specific protein thought to be located on the sperm surface. Functional studies in the mouse revealed that loss of PKDREJ has effects on sperm transport and the ability to undergo an induced acrosome reaction. Thus, PKDREJ has been considered a potential target of post-copulatory sexual selection in the form of sperm competition. Proteins involved in reproductive processes often show accelerated evolution. In many cases, this rapid divergence is promoted by positive selection which may be driven, at least in part, by post-copulatory sexual selection. We analysed the evolution of the PKDREJ protein in primates and rodents and assessed whether PKDREJ divergence is associated with testes mass relative to body mass, which is a reliable proxy of sperm competition levels. Evidence of an association between the evolutionary rate of the PKDREJ gene and testes mass relative to body mass was not found in primates. Among rodents, evidence of positive selection was detected in the Pkdrej gene in the family Cricetidae but not in Muridae. We then assessed whether Pkdrej divergence is associated with episodes of sperm competition in these families. We detected a positive significant correlation between the evolutionary rates of Pkdrej and testes mass relative to body mass in cricetids. These findings constitute the first evidence of post-copulatory sexual selection influencing the evolution of a protein that participates in the mechanisms regulating sperm transport and the acrosome reaction, strongly suggesting that positive selection may act on these fertilization steps, leading to advantages in situations of sperm competition. PMID:25304980

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

PubMed Central

Linkeviciute, Viktorija; Rackham, Owen J.L.; Gough, Julian; Oates, Matt E.; Fang, Hai

2015-01-01

To help evaluate how protein function impacts on genome evolution, we introduce a new concept of ‘architecture plasticity potential’ – the capacity to form distinct domain architectures – both for an individual domain, or more generally for a set of domains grouped by shared function. We devise a scoring metric to measure the plasticity potential for these domain sets, and evaluate how function has changed over time for different species. Applying this metric to a phylogenetic tree of eukaryotic genomes, we find that the involvement of each function is not random but highly selective. For certain lineages there is strong bias for evolution to involve domains related to certain functions. In general eukaryotic genomes, particularly animals, expand complex functional activities such as signalling and regulation, but at the cost of reducing metabolic processes. We also observe differential evolution of transcriptional regulation and a unique evolutionary role of channel regulators; crucially this is only observable in terms of the architecture plasticity potential. Our findings provide a new layer of information to understand the significance of function in eukaryotic genome evolution. A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution. PMID:25980317

Kin selection and the evolution of plant reproductive traits.

PubMed

Bawa, Kamaljit S

2016-11-16

Competition among developing seeds and sibling rivalry within multiovulated ovaries can be deleterious for both the maternal parent and the siblings. Increased genetic relatedness of seeds within the ovary may foster kin selection and reduce the deleterious consequences of sibling competition. The pollen parent may also be selected for siring all progeny within a fruit. I propose a series of hypotheses to explain the evolution of a number of reproductive traits in angiosperms in the context of kin selection and sibling rivalry within the ovaries of angiosperms. I present evidence to show that a single-pollen parent, indeed, often sires seeds within multiovulated ovaries. Various types of pollen aggregations and transfer of such pollen masses to the stigmas of flowers by specialized pollinators make this increased genetic relatedness possible. An alternative mode to reduce sibling rivalry may be the reduction of ovule number to one, an evolutionary trend that has independently occurred many times in flowering plants. Finally, I build on previously established correlations to predict two sets of correlations among reproductive traits. In the first case, large showy flowers, transfer of pollen en masse by specialized pollinators, and multiovulated ovaries and multisided fruits seem to be correlated. In the second case, the previously established correlations among small and inconspicuous flowers, pollination by wind, water or generalist insects, flowers and fruits with few or single ovules and seeds, respectively, may also include monoecy or dioecy. Although correlations among many of these traits have been established in the past, I invoke kin selection and sibling competition to explain the evolution of correlated traits as two distinct evolutionary pathways in angiosperms. © 2016 The Authors.

Kin selection and the evolution of plant reproductive traits

PubMed Central

Bawa, Kamaljit S.

2016-01-01

Competition among developing seeds and sibling rivalry within multiovulated ovaries can be deleterious for both the maternal parent and the siblings. Increased genetic relatedness of seeds within the ovary may foster kin selection and reduce the deleterious consequences of sibling competition. The pollen parent may also be selected for siring all progeny within a fruit. I propose a series of hypotheses to explain the evolution of a number of reproductive traits in angiosperms in the context of kin selection and sibling rivalry within the ovaries of angiosperms. I present evidence to show that a single-pollen parent, indeed, often sires seeds within multiovulated ovaries. Various types of pollen aggregations and transfer of such pollen masses to the stigmas of flowers by specialized pollinators make this increased genetic relatedness possible. An alternative mode to reduce sibling rivalry may be the reduction of ovule number to one, an evolutionary trend that has independently occurred many times in flowering plants. Finally, I build on previously established correlations to predict two sets of correlations among reproductive traits. In the first case, large showy flowers, transfer of pollen en masse by specialized pollinators, and multiovulated ovaries and multisided fruits seem to be correlated. In the second case, the previously established correlations among small and inconspicuous flowers, pollination by wind, water or generalist insects, flowers and fruits with few or single ovules and seeds, respectively, may also include monoecy or dioecy. Although correlations among many of these traits have been established in the past, I invoke kin selection and sibling competition to explain the evolution of correlated traits as two distinct evolutionary pathways in angiosperms. PMID:27852800

Selection to outsmart the germs: The evolution of disease recognition and social cognition.

PubMed

Kessler, Sharon E; Bonnell, Tyler R; Byrne, Richard W; Chapman, Colin A

2017-07-01

The emergence of providing care to diseased conspecifics must have been a turning point during the evolution of hominin sociality. On a population level, care may have minimized the costs of socially transmitted diseases at a time of increasing social complexity, although individual care-givers probably incurred increased transmission risks. We propose that care-giving likely originated within kin networks, where the costs may have been balanced by fitness increases obtained through caring for ill kin. We test a novel hypothesis of hominin cognitive evolution in which disease may have selected for the cognitive ability to recognize when a conspecific is infected. Because diseases may produce symptoms that are likely detectable via the perceptual-cognitive pathways integral to social cognition, we suggest that disease recognition and social cognition may have evolved together. Using agent-based modeling, we test 1) under what conditions disease can select for increasing disease recognition and care-giving among kin, 2) whether providing care produces greater selection for cognition than an avoidance strategy, and 3) whether care-giving alters the progression of the disease through the population. The greatest selection was produced by diseases with lower risks to the care-giver and prevalences low enough not to disrupt the kin networks. When care-giving and avoidance strategies were compared, only care-giving reduced the severity of the disease outbreaks and subsequent population crashes. The greatest selection for increased cognitive abilities occurred early in the model runs when the outbreaks and population crashes were most severe. Therefore, over the course of human evolution, repeated introductions of novel diseases into naïve populations could have produced sustained selection for increased disease recognition and care-giving behavior, leading to the evolution of increased cognition, social complexity, and, eventually, medical care in humans. Finally, we lay

An organismic critique of molecular darwinism.

PubMed

Wicken, J S

1985-12-21

The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.

Extremal Optimization: Methods Derived from Co-Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boettcher, S.; Percus, A.G.

1999-07-13

We describe a general-purpose method for finding high-quality solutions to hard optimization problems, inspired by self-organized critical models of co-evolution such as the Bak-Sneppen model. The method, called Extremal Optimization, successively eliminates extremely undesirable components of sub-optimal solutions, rather than ''breeding'' better components. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, Extremal Optimization improves on a single candidate solution by treating each of its components as species co-evolving according to Darwinian principles. Unlike Simulated Annealing, its non-equilibrium approach effects an algorithm requiring few parameters to tune. With only one adjustable parameter, its performance provesmore » competitive with, and often superior to, more elaborate stochastic optimization procedures. We demonstrate it here on two classic hard optimization problems: graph partitioning and the traveling salesman problem.« less

Digit loss in archosaur evolution and the interplay between selection and constraints.

PubMed

de Bakker, Merijn A G; Fowler, Donald A; den Oude, Kelly; Dondorp, Esther M; Navas, M Carmen Garrido; Horbanczuk, Jaroslaw O; Sire, Jean-Yves; Szczerbińska, Danuta; Richardson, Michael K

2013-08-22

Evolution involves interplay between natural selection and developmental constraints. This is seen, for example, when digits are lost from the limbs during evolution. Extant archosaurs (crocodiles and birds) show several instances of digit loss under different selective regimes, and show limbs with one, two, three, four or the ancestral number of five digits. The 'lost' digits sometimes persist for millions of years as developmental vestiges. Here we examine digit loss in the Nile crocodile and five birds, using markers of three successive stages of digit development. In two independent lineages under different selection, wing digit I and all its markers disappear. In contrast, hindlimb digit V persists in all species sampled, both as cartilage, and as Sox9- expressing precartilage domains, 250 million years after the adult digit disappeared. There is therefore a mismatch between evolution of the embryonic and adult phenotypes. All limbs, regardless of digit number, showed similar expression of sonic hedgehog (Shh). Even in the one-fingered emu wing, expression of posterior genes Hoxd11 and Hoxd12 was conserved, whereas expression of anterior genes Gli3 and Alx4 was not. We suggest that the persistence of digit V in the embryo may reflect constraints, particularly the conserved posterior gene networks associated with the zone of polarizing activity (ZPA). The more rapid and complete disappearance of digit I may reflect its ZPA-independent specification, and hence, weaker developmental constraints. Interacting with these constraints are selection pressures for limb functions such as flying and perching. This model may help to explain the diverse patterns of digit loss in tetrapods. Our study may also help to understand how selection on adults leads to changes in development.

Selection platforms for directed evolution in synthetic biology.

PubMed

Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

2016-08-15

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

Evolution of brain region volumes during artificial selection for relative brain size.

PubMed

Kotrschal, Alexander; Zeng, Hong-Li; van der Bijl, Wouter; Öhman-Mägi, Caroline; Kotrschal, Kurt; Pelckmans, Kristiaan; Kolm, Niclas

2017-12-01

The vertebrate brain shows an extremely conserved layout across taxa. Still, the relative sizes of separate brain regions vary markedly between species. One interesting pattern is that larger brains seem associated with increased relative sizes only of certain brain regions, for instance telencephalon and cerebellum. Till now, the evolutionary association between separate brain regions and overall brain size is based on comparative evidence and remains experimentally untested. Here, we test the evolutionary response of brain regions to directional selection on brain size in guppies (Poecilia reticulata) selected for large and small relative brain size. In these animals, artificial selection led to a fast response in relative brain size, while body size remained unchanged. We use microcomputer tomography to investigate how the volumes of 11 main brain regions respond to selection for larger versus smaller brains. We found no differences in relative brain region volumes between large- and small-brained animals and only minor sex-specific variation. Also, selection did not change allometric scaling between brain and brain region sizes. Our results suggest that brain regions respond similarly to strong directional selection on relative brain size, which indicates that brain anatomy variation in contemporary species most likely stem from direct selection on key regions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Endosymbiosis and its implications for evolutionary theory.

PubMed

O'Malley, Maureen A

2015-08-18

Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics "follows" genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation.

Feedback between environment and traits under selection in a seasonal environment: consequences for experimental evolution.

PubMed

Collot, Dorian; Nidelet, Thibault; Ramsayer, Johan; Martin, Olivier C; Méléard, Sylvie; Dillmann, Christine; Sicard, Delphine; Legrand, Judith

2018-04-11

Batch cultures are frequently used in experimental evolution to study the dynamics of adaptation. Although they are generally considered to simply drive a growth rate increase, other fitness components can also be selected for. Indeed, recurrent batches form a seasonal environment where different phases repeat periodically and different traits can be under selection in the different seasons. Moreover, the system being closed, organisms may have a strong impact on the environment. Thus, the study of adaptation should take into account the environment and eco-evolutionary feedbacks. Using data from an experimental evolution on yeast Saccharomyces cerevisiae , we developed a mathematical model to understand which traits are under selection, and what is the impact of the environment for selection in a batch culture. We showed that two kinds of traits are under selection in seasonal environments: life-history traits, related to growth and mortality, but also transition traits, related to the ability to react to environmental changes. The impact of environmental conditions can be summarized by the length of the different seasons which weight selection on each trait: the longer a season is, the higher the selection on associated traits. Since phenotypes drive season length, eco-evolutionary feedbacks emerge. Our results show how evolution in successive batches can affect season lengths and strength of selection on different traits. © 2018 The Author(s).

Genetic evolution, plasticity, and bet-hedging as adaptive responses to temporally autocorrelated fluctuating selection: A quantitative genetic model.

PubMed

Tufto, Jarle

2015-08-01

Adaptive responses to autocorrelated environmental fluctuations through evolution in mean reaction norm elevation and slope and an independent component of the phenotypic variance are analyzed using a quantitative genetic model. Analytic approximations expressing the mutual dependencies between all three response modes are derived and solved for the joint evolutionary outcome. Both genetic evolution in reaction norm elevation and plasticity are favored by slow temporal fluctuations, with plasticity, in the absence of microenvironmental variability, being the dominant evolutionary outcome for reasonable parameter values. For fast fluctuations, tracking of the optimal phenotype through genetic evolution and plasticity is limited. If residual fluctuations in the optimal phenotype are large and stabilizing selection is strong, selection then acts to increase the phenotypic variance (bet-hedging adaptive). Otherwise, canalizing selection occurs. If the phenotypic variance increases with plasticity through the effect of microenvironmental variability, this shifts the joint evolutionary balance away from plasticity in favor of genetic evolution. If microenvironmental deviations experienced by each individual at the time of development and selection are correlated, however, more plasticity evolves. The adaptive significance of evolutionary fluctuations in plasticity and the phenotypic variance, transient evolution, and the validity of the analytic approximations are investigated using simulations. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

From Homo Sapiens to Homo Cosmicus - Astronautics, Darwinism abd Historical Determinism

NASA Astrophysics Data System (ADS)

Tolkowsky, G.

Since its inception in late-nineteenth century, astronautics has been viewed as a historical outcome of human evolution as well as a future driver thereof. The history of astronautics-related, evolutionary thought reveals a tension between the Darwinian notion of natural selection and that of homocosmic predestination - be it of dialectical materialistic or theological nature. One can detect the influence of this ideological diversity on the American and Soviet space programs.

Handgrip Strength as a Darwinian Fitness Indicator in Men

PubMed Central

Gallup, Andrew C.; Fink, Bernhard

2018-01-01

Handgrip strength (HGS) is a robust measure of overall muscular strength and function, and has long been predictive of a multitude of health factors and physical outcomes for both men and women. The fact that HGS represents such a ubiquitous measure of health and vitality may reflect the significance of this trait during human evolution. This trait is also highly sexually dimorphic due to influences of androgenic hormones and fat-free body mass, suggesting that it has been further elaborated through sexual selection. Consistent with this view, research within evolutionary psychology and related fields has documented distinct relationships between HGS and measures of social and sexual behavior, especially in men. Here, we review studies across different societies and cultural contexts showing that male HGS predicts measures of aggression and social dominance, perceived formidability, male-typical body morphology and movement, courtship display, physical attractiveness, and sexual behavior and reproductive fitness. These findings underscore the value of including HGS as an independent measure within studies examining human sexual selection, and corroborate existing research suggesting that specific features of physical strength have and continue to be under positive directional selection in men. PMID:29681871

Handgrip Strength as a Darwinian Fitness Indicator in Men.

PubMed

Gallup, Andrew C; Fink, Bernhard

2018-01-01

Handgrip strength (HGS) is a robust measure of overall muscular strength and function, and has long been predictive of a multitude of health factors and physical outcomes for both men and women. The fact that HGS represents such a ubiquitous measure of health and vitality may reflect the significance of this trait during human evolution. This trait is also highly sexually dimorphic due to influences of androgenic hormones and fat-free body mass, suggesting that it has been further elaborated through sexual selection. Consistent with this view, research within evolutionary psychology and related fields has documented distinct relationships between HGS and measures of social and sexual behavior, especially in men. Here, we review studies across different societies and cultural contexts showing that male HGS predicts measures of aggression and social dominance, perceived formidability, male-typical body morphology and movement, courtship display, physical attractiveness, and sexual behavior and reproductive fitness. These findings underscore the value of including HGS as an independent measure within studies examining human sexual selection, and corroborate existing research suggesting that specific features of physical strength have and continue to be under positive directional selection in men.

Levels and limits in artificial selection of communities.

PubMed

Blouin, Manuel; Karimi, Battle; Mathieu, Jérôme; Lerch, Thomas Z

2015-10-01

Artificial selection of individuals has been determinant in the elaboration of the Darwinian theory of natural selection. Nowadays, artificial selection of ecosystems has proven its efficiency and could contribute to a theory of natural selection at several organisation levels. Here, we were not interested in identifying mechanisms of adaptation to selection, but in establishing the proof of principle that a specific structure of interaction network emerges under ecosystem artificial selection. We also investigated the limits in ecosystem artificial selection to evaluate its potential in terms of managing ecosystem function. By artificially selecting microbial communities for low CO2 emissions over 21 generations (n = 7560), we found a very high heritability of community phenotype (52%). Artificial selection was responsible for simpler interaction networks with lower interaction richness. Phenotype variance and heritability both decreased across generations, suggesting that selection was more likely limited by sampling effects than by stochastic ecosystem dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

Density-dependent selection on mate search and evolution of Allee effects.

PubMed

Berec, Luděk; Kramer, Andrew M; Bernhauerová, Veronika; Drake, John M

2018-01-01

Sexually reproducing organisms require males and females to find each other. Increased difficulty of females finding mates as male density declines is the most frequently reported mechanism of Allee effects in animals. Evolving more effective mate search may alleviate Allee effects, but may depend on density regimes a population experiences. In particular, high-density populations may evolve mechanisms that induce Allee effects which become detrimental when populations are reduced and maintained at a low density. We develop an individual-based, eco-genetic model to study how mating systems and fitness trade-offs interact with changes in population density to drive evolution of the rate at which males or females search for mates. Finite mate search rate triggers Allee effects in our model and we explore how these Allee effects respond to such evolution. We allow a population to adapt to several population density regimes and examine whether high-density populations are likely to reverse adaptations attained at low densities. We find density-dependent selection in most of scenarios, leading to search rates that result in lower Allee thresholds in populations kept at lower densities. This mainly occurs when fecundity costs are imposed on mate search, and provides an explanation for why Allee effects are often observed in anthropogenically rare species. Optimizing selection, where the attained trait value minimizes the Allee threshold independent of population density, depended on the trade-off between search and survival, combined with monogamy when females were searching. Other scenarios led to runaway selection on the mate search rate, including evolutionary suicide. Trade-offs involved in mate search may thus be crucial to determining how density influences the evolution of Allee effects. Previous studies did not examine evolution of a trait related to the strength of Allee effects under density variation. We emphasize the crucial role that mating systems, fitness

Nothing in the History of Spanish Anís Makes Sense, Except in the Light of Evolution

NASA Astrophysics Data System (ADS)

Delgado, Juan Antonio; Palma, Ricardo Luis

2011-02-01

We describe, discuss and illustrate a metaphoric parallel between the history of the most famous Spanish liqueur, " Anís del Mono" ( Anís of the Monkey), and the evolution of living organisms in the light of Darwinian theory and other biological hypotheses published subsequent to Charles Darwin's Origin of Species. Also, we report the use of a caricature of a simian Darwin with a positive connotation, perhaps the only one ever produced. We conclude that, like some species in the natural world, Anís of the Monkey has evolved, adapted, survived and become the fittest and most successful anís in the Spanish market and possibly the world. We hope this paper will contribute a new useful metaphor for the teaching of biological evolution.

Multilevel selection and social evolution of insect societies

NASA Astrophysics Data System (ADS)

Korb, Judith; Heinze, Jürgen

How sterile, altruistic worker castes have evolved in social insects and how they are maintained have long been central topics in evolutionary biology. With the advance of kin selection theory, insect societies, in particular those of haplodiploid bees, ants, and wasps, have become highly suitable model systems for investigating the details of social evolution and recently also how within-group conflicts are resolved. Because insect societies typically do not consist of clones, conflicts among nestmates arise, for example about the partitioning of reproduction and the allocation of resources towards male and female sexuals. Variation in relatedness among group members therefore appears to have a profound influence on the social structure of groups. However, insect societies appear to be remarkably robust against such variation: division of labor and task allocation are often organized in more or less the same way in societies with high as in those with very low nestmate relatedness. To explain the discrepancy between predictions from kin structure and empirical data, it was suggested that constraints-such as the lack of power or information-prevent individuals from pursuing their own selfish interests. Applying a multilevel selection approach shows that these constraints are in fact group-level adaptation preventing or resolving intracolonial conflict. The mechanisms of conflict resolution in insect societies are similar to those at other levels in the biological hierarchy (e.g., in the genome or multicellular organisms): alignment of interests, fair lottery, and social control. Insect societies can thus be regarded as a level of selection with novelties that provide benefits beyond the scope of a solitary life. Therefore, relatedness is less important for the maintenance of insect societies, although it played a fundamental role in their evolution.

The effect of selection environment on the probability of parallel evolution.

PubMed

Bailey, Susan F; Rodrigue, Nicolas; Kassen, Rees

2015-06-01

Across the great diversity of life, there are many compelling examples of parallel and convergent evolution-similar evolutionary changes arising in independently evolving populations. Parallel evolution is often taken to be strong evidence of adaptation occurring in populations that are highly constrained in their genetic variation. Theoretical models suggest a few potential factors driving the probability of parallel evolution, but experimental tests are needed. In this study, we quantify the degree of parallel evolution in 15 replicate populations of Pseudomonas fluorescens evolved in five different environments that varied in resource type and arrangement. We identified repeat changes across multiple levels of biological organization from phenotype, to gene, to nucleotide, and tested the impact of 1) selection environment, 2) the degree of adaptation, and 3) the degree of heterogeneity in the environment on the degree of parallel evolution at the gene-level. We saw, as expected, that parallel evolution occurred more often between populations evolved in the same environment; however, the extent of parallel evolution varied widely. The degree of adaptation did not significantly explain variation in the extent of parallelism in our system but number of available beneficial mutations correlated negatively with parallel evolution. In addition, degree of parallel evolution was significantly higher in populations evolved in a spatially structured, multiresource environment, suggesting that environmental heterogeneity may be an important factor constraining adaptation. Overall, our results stress the importance of environment in driving parallel evolutionary changes and point to a number of avenues for future work for understanding when evolution is predictable. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The genomics of selection in dogs and the parallel evolution between dogs and humans.

PubMed

Wang, Guo-dong; Zhai, Weiwei; Yang, He-chuan; Fan, Ruo-xi; Cao, Xue; Zhong, Li; Wang, Lu; Liu, Fei; Wu, Hong; Cheng, Lu-guang; Poyarkov, Andrei D; Poyarkov, Nikolai A; Tang, Shu-sheng; Zhao, Wen-ming; Gao, Yun; Lv, Xue-mei; Irwin, David M; Savolainen, Peter; Wu, Chung-I; Zhang, Ya-ping

2013-01-01

The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.

Sexual selection affects the evolution of lifespan and ageing in the decorated cricket Gryllodes sigillatus.

PubMed

Archer, C R; Zajitschek, F; Sakaluk, S K; Royle, N J; Hunt, J

2012-10-01

Recent work suggests that sexual selection can influence the evolution of ageing and lifespan by shaping the optimal timing and relative costliness of reproductive effort in the sexes. We used inbred lines of the decorated cricket, Gryllodes sigillatus, to estimate the genetic (co)variance between age-dependent reproductive effort, lifespan, and ageing within and between the sexes. Sexual selection theory predicts that males should die sooner and age more rapidly than females. However, a reversal of this pattern may be favored if reproductive effort increases with age in males but not in females. We found that male calling effort increased with age, whereas female fecundity decreased, and that males lived longer and aged more slowly than females. These divergent life-history strategies were underpinned by a positive genetic correlation between early-life reproductive effort and ageing rate in both sexes, although this relationship was stronger in females. Despite these sex differences in life-history schedules, age-dependent reproductive effort, lifespan, and ageing exhibited strong positive intersexual genetic correlations. This should, in theory, constrain the independent evolution of these traits in the sexes and may promote intralocus sexual conflict. Our study highlights the importance of sexual selection to the evolution of sex differences in ageing and lifespan in G. sigillatus. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Adaptive evolution of insect selective excitatory β-type sodium channel neurotoxins from scorpion venom.

PubMed

Wu, Wenlan; Li, Zhongjie; Ma, Yibao

2017-06-01

Insect selective excitatory β-type sodium channel neurotoxins from scorpion venom (β-NaScTxs) are composed of about 70-76 amino acid residues and share a common scaffold stabilized by four unique disulfide bonds. The phylogenetic analysis of these toxins was hindered by limited sequence data. In our recent study, two new insect selective excitatory β-NaScTxs, LmIT and ImIT, were isolated from Lychas mucronatus and Isometrus maculatus, respectively. With the sequences previously reported, we examined the adaptive molecular evolution of insect selective excitatory β-NaScTxs by estimating the nonsynonymous-to-synonymous rate ratio (ω=d N /d S ). The results revealed 12 positively selected sites in the genes of insect selective excitatory β-NaScTxs. Moreover, these positively selected sites match well with the sites important for interacting with sodium channels, as demonstrated in previous mutagenesis study. These results reveal that adaptive evolution after gene duplication is one of the most important genetic mechanisms of scorpion neurotoxin diversification. Copyright © 2017 Elsevier Inc. All rights reserved.

Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection.

PubMed

Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

2013-11-01

Replicated selection experiments provide a powerful way to study how "multiple adaptive solutions" may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n=17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between sexes and among the four selected lines. Analyses of litter size and realized selection differentials seem to rule out counterposing natural selection as a cause of the selection limits. Animal-model analyses showed that although the additive genetic variance was significantly lower in selected than control lines, both before and after the limits, the decrease was not sufficient to explain the limits. Moreover, directional selection promoted a negative covariance between additive and maternal genetic variance over the first 10 generations. These results stress the importance of replication in selection studies of higher-level traits and highlight the fact that long-term predictions of response to selection are not necessarily expected to be linear because of the variable effects of selection on additive genetic variance and maternal effects. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

The Theory of Evolution - A Jewish Perspective

PubMed Central

Steinberg, Avraham

2010-01-01

All possible pro and con arguments regarding the theory of evolution have been discussed and debated in the vast literature—scientific, religious, and lay—in the past 150 years. There is usually great zealotry in all debating parties, with mutual intolerance of ideas and concepts, disrespect toward opposing opinions and positions, and usage of very harsh language. This prejudiced approach usually does not allow for a reasonable debate. It is important to look at the facts, assumptions, and beliefs of the theory of evolution in a more calm and humble way. In this article a comparative analysis is offered between the scientific aspects of the theory of evolution and a Judaic approach to these aspects. The two sets of human thought—religion and science—are fundamentally different in their aims and purposes, in their methods of operation, in their scope of interest and issues, and in their origin and ramifications. Whenever science surpasses its limits, or religion exceeds its boundaries, it actually is a form of an abuse of both. This has happened to the theory of evolution in a more powerful mode than any other interaction between science and religion. The agenda of many scientists who promote the theory of evolution is to achieve the goal of understanding the existence of the universe as a random, purposeless, natural development, evolved slowly over billions of years from a common ancestor by way of natural selection, devoid of any supernatural metaphysical power. Jewish faith perceives the development of the universe in a different way: God created the world, with a purpose known to Him; He established natural laws that govern the world; and He imposed a moral-religious set of requirements upon Man. The discussion and comparative analysis in this article is based upon the current neo-Darwinian theory, although it seems almost certain that even the new and modern assumptions and speculations will continue to be challenged, changed, and revised as new

The theory of evolution - a jewish perspective.

PubMed

Steinberg, Avraham

2010-07-01

All possible pro and con arguments regarding the theory of evolution have been discussed and debated in the vast literature-scientific, religious, and lay-in the past 150 years. There is usually great zealotry in all debating parties, with mutual intolerance of ideas and concepts, disrespect toward opposing opinions and positions, and usage of very harsh language. This prejudiced approach usually does not allow for a reasonable debate. It is important to look at the facts, assumptions, and beliefs of the theory of evolution in a more calm and humble way. In this article a comparative analysis is offered between the scientific aspects of the theory of evolution and a Judaic approach to these aspects. The two sets of human thought-religion and science-are fundamentally different in their aims and purposes, in their methods of operation, in their scope of interest and issues, and in their origin and ramifications. Whenever science surpasses its limits, or religion exceeds its boundaries, it actually is a form of an abuse of both. This has happened to the theory of evolution in a more powerful mode than any other interaction between science and religion. The agenda of many scientists who promote the theory of evolution is to achieve the goal of understanding the existence of the universe as a random, purposeless, natural development, evolved slowly over billions of years from a common ancestor by way of natural selection, devoid of any supernatural metaphysical power. JEWISH FAITH PERCEIVES THE DEVELOPMENT OF THE UNIVERSE IN A DIFFERENT WAY: God created the world, with a purpose known to Him; He established natural laws that govern the world; and He imposed a moral-religious set of requirements upon Man. The discussion and comparative analysis in this article is based upon the current neo-Darwinian theory, although it seems almost certain that even the new and modern assumptions and speculations will continue to be challenged, changed, and revised as new scientific

Müllerian and Batesian mimicry out, Darwinian and Wallacian mimicry in, for rewarding/rewardless flowers.

PubMed

Lev-Yadun, Simcha

2018-06-11

Müllerian and Batesian mimicry were originally defined in defensive (anti-predetory) animal systems. Later these terms were adopted by botanists studying pollination that defined rewarding flowers as Müllerian mimics and rewardless flowers as Batesian mimics. The use of these terms concerning pollination predated our recent understanding of how common plant aposematism is and the related defensive Müllerian and Batesian mimicry types. Being non-defensive, using the terms Müllerian and Batesian mimicry for rewarding/rewardless flowers is, however, confusing if not misleading, and is also logically inappropriate. I suggest to first stop using the terms Batesian and Müllerian mimicry concerning rewarding/rewardless flowers and pollination, and second, to define the guild of flowers that reward pollinatiors as Darwinian mimics and those that do not reward pollinators as Wallacian mimics.

Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.

PubMed

Franssen, Susanne U; Barton, Nicholas H; Schlötterer, Christian

2017-01-01

The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

On the levels of enzymatic substrate specificity: Implications for the early evolution of metabolic pathways

NASA Technical Reports Server (NTRS)

Lazcano, A.; Diaz-Villagomez, E.; Mills, T.; Oro, J.

1995-01-01

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called 'patchwork' theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.

Fluctuating environments, sexual selection and the evolution of flexible mate choice in birds.

PubMed

Botero, Carlos A; Rubenstein, Dustin R

2012-01-01

Environmentally-induced fluctuation in the form and strength of natural selection can drive the evolution of morphology, physiology, and behavior. Here we test the idea that fluctuating climatic conditions may also influence the process of sexual selection by inducing unexpected reversals in the relative quality or sexual attractiveness of potential breeding partners. Although this phenomenon, known as 'ecological cross-over', has been documented in a variety of species, it remains unclear the extent to which it has driven the evolution of major interspecific differences in reproductive behavior. We show that after controlling for potentially influential life history and demographic variables, there are significant positive associations between the variability and predictability of annual climatic cycles and the prevalence of infidelity and divorce within populations of a taxonomically diverse array of socially monogamous birds. Our results are consistent with the hypothesis that environmental factors have shaped the evolution of reproductive flexibility and suggest that in the absence of severe time constraints, secondary mate choice behaviors can help prevent, correct, or minimize the negative consequences of ecological cross-overs. Our findings also illustrate how a basic evolutionary process like sexual selection is susceptible to the increasing variability and unpredictability of climatic conditions that is resulting from climate change.

Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies.

PubMed

Mina, Marco; Raynaud, Franck; Tavernari, Daniele; Battistello, Elena; Sungalee, Stephanie; Saghafinia, Sadegh; Laessle, Titouan; Sanchez-Vega, Francisco; Schultz, Nikolaus; Oricchio, Elisa; Ciriello, Giovanni

2017-08-14

Cancer evolves through the emergence and selection of molecular alterations. Cancer genome profiling has revealed that specific events are more or less likely to be co-selected, suggesting that the selection of one event depends on the others. However, the nature of these evolutionary dependencies and their impact remain unclear. Here, we designed SELECT, an algorithmic approach to systematically identify evolutionary dependencies from alteration patterns. By analyzing 6,456 genomes from multiple tumor types, we constructed a map of oncogenic dependencies associated with cellular pathways, transcriptional readouts, and therapeutic response. Finally, modeling of cancer evolution shows that alteration dependencies emerge only under conditional selection. These results provide a framework for the design of strategies to predict cancer progression and therapeutic response. Copyright © 2017 Elsevier Inc. All rights reserved.

Sexual selection and the adaptive evolution of PKDREJ protein in primates and rodents.

PubMed

Vicens, Alberto; Gómez Montoto, Laura; Couso-Ferrer, Francisco; Sutton, Keith A; Roldan, Eduardo R S

2015-02-01

PKDREJ is a testis-specific protein thought to be located on the sperm surface. Functional studies in the mouse revealed that loss of PKDREJ has effects on sperm transport and the ability to undergo an induced acrosome reaction. Thus, PKDREJ has been considered a potential target of post-copulatory sexual selection in the form of sperm competition. Proteins involved in reproductive processes often show accelerated evolution. In many cases, this rapid divergence is promoted by positive selection which may be driven, at least in part, by post-copulatory sexual selection. We analysed the evolution of the PKDREJ protein in primates and rodents and assessed whether PKDREJ divergence is associated with testes mass relative to body mass, which is a reliable proxy of sperm competition levels. Evidence of an association between the evolutionary rate of the PKDREJ gene and testes mass relative to body mass was not found in primates. Among rodents, evidence of positive selection was detected in the Pkdrej gene in the family Cricetidae but not in Muridae. We then assessed whether Pkdrej divergence is associated with episodes of sperm competition in these families. We detected a positive significant correlation between the evolutionary rates of Pkdrej and testes mass relative to body mass in cricetids. These findings constitute the first evidence of post-copulatory sexual selection influencing the evolution of a protein that participates in the mechanisms regulating sperm transport and the acrosome reaction, strongly suggesting that positive selection may act on these fertilization steps, leading to advantages in situations of sperm competition. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evolutionary ethnobiology and cultural evolution: opportunities for research and dialog.

PubMed

Santoro, Flávia Rosa; Nascimento, André Luiz Borba; Soldati, Gustavo Taboada; Ferreira Júnior, Washington Soares; Albuquerque, Ulysses Paulino

2018-01-09

The interest in theoretical frameworks that improve our understanding of social-ecological systems is growing within the field of ethnobiology. Several evolutionary questions may underlie the relationships between people and the natural resources that are investigated in this field. A new branch of research, known as evolutionary ethnobiology (EE), focuses on these questions and has recently been formally conceptualized. The field of cultural evolution (CE) has significantly contributed to the development of this new field, and it has introduced the Darwinian concepts of variation, competition, and heredity to studies that focus on the dynamics of local knowledge. In this article, we introduce CE as an important theoretical framework for evolutionary ethnobiological research. We present the basic concepts and assumptions of CE, along with the adjustments that are necessary for its application in EE. We discuss different ethnobiological studies in the context of this new framework and the new opportunities for research that exist in this area. We also propose a dialog that includes our findings in the context of cultural evolution.

A model of directional selection applied to the evolution of drug resistance in HIV-1.

PubMed

Seoighe, Cathal; Ketwaroo, Farahnaz; Pillay, Visva; Scheffler, Konrad; Wood, Natasha; Duffet, Rodger; Zvelebil, Marketa; Martinson, Neil; McIntyre, James; Morris, Lynn; Hide, Winston

2007-04-01

Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the neutral rate. Rapid evolution at sites that confer resistance to drugs can be used to help elucidate the mechanisms of evolution of drug resistance and to discover or corroborate novel resistance mutations. We have implemented standard maximum likelihood methods that are used to detect diversifying selection and adapted them for use with serially sampled reverse transcriptase (RT) coding sequences isolated from a group of 300 HIV-1 subtype C-infected women before and after single-dose nevirapine (sdNVP) to prevent mother-to-child transmission. We have also extended the standard models of codon evolution for application to the detection of directional selection. Through simulation, we show that the directional selection model can provide a substantial improvement in sensitivity over models of diversifying selection. Five of the sites within the RT gene that are known to harbor mutations that confer resistance to nevirapine (NVP) strongly supported the directional selection model. There was no evidence that other mutations that are known to confer NVP resistance were selected in this cohort. The directional selection model, applied to serially sampled sequences, also had more power than the diversifying selection model to detect selection resulting from factors other than drug resistance. Because inference of selection from serial samples is unlikely to be adversely affected by recombination, the methods we describe may have general applicability to the analysis of positive selection affecting recombining coding sequences when serially sampled data are available.

FOXP2 targets show evidence of positive selection in European populations.

PubMed

Ayub, Qasim; Yngvadottir, Bryndis; Chen, Yuan; Xue, Yali; Hu, Min; Vernes, Sonja C; Fisher, Simon E; Tyler-Smith, Chris

2013-05-02

Forkhead box P2 (FOXP2) is a highly conserved transcription factor that has been implicated in human speech and language disorders and plays important roles in the plasticity of the developing brain. The pattern of nucleotide polymorphisms in FOXP2 in modern populations suggests that it has been the target of positive (Darwinian) selection during recent human evolution. In our study, we searched for evidence of selection that might have followed FOXP2 adaptations in modern humans. We examined whether or not putative FOXP2 targets identified by chromatin-immunoprecipitation genomic screening show evidence of positive selection. We developed an algorithm that, for any given gene list, systematically generates matched lists of control genes from the Ensembl database, collates summary statistics for three frequency-spectrum-based neutrality tests from the low-coverage resequencing data of the 1000 Genomes Project, and determines whether these statistics are significantly different between the given gene targets and the set of controls. Overall, there was strong evidence of selection of FOXP2 targets in Europeans, but not in the Han Chinese, Japanese, or Yoruba populations. Significant outliers included several genes linked to cellular movement, reproduction, development, and immune cell trafficking, and 13 of these constituted a significant network associated with cardiac arteriopathy. Strong signals of selection were observed for CNTNAP2 and RBFOX1, key neurally expressed genes that have been consistently identified as direct FOXP2 targets in multiple studies and that have themselves been associated with neurodevelopmental disorders involving language dysfunction. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Student Conceptions of Natural Selection and Its Role in Evolution, Research Series No. l65.

ERIC Educational Resources Information Center

Bishop, Beth A.; Anderson, Charles W.

Pretests and posttests on the topic of evolution through natural selection were administered to students in a college nonmajors' biology course. Analysis of test responses revealed that most students understood evolution as a process in which species respond to environmental conditions by changing gradually over time. Student thinking differed…

The scope and strength of sex-specific selection in genome evolution

PubMed Central

Wright, A E; Mank, J E

2013-01-01

Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. PMID:23848139

Nonmathematical models for evolution of altruism, and for group selection (peck order-territoriality-ant colony-dual-determinant model-tri-determinant model).

PubMed

Darlington, P J

1972-02-01

Mathematical biologists have failed to produce a satisfactory general model for evolution of altruism, i.e., of behaviors by which "altruists" benefit other individuals but not themselves; kin selection does not seem to be a sufficient explanation of nonreciprocal altruism. Nonmathematical (but mathematically acceptable) models are now proposed for evolution of negative altruism in dual-determinant and of positive altruism in tri-determinant systems. Peck orders, territorial systems, and an ant society are analyzed as examples. In all models, evolution is primarily by individual selection, probably supplemented by group selection. Group selection is differential extinction of populations. It can act only on populations preformed by selection at the individual level, but can either cancel individual selective trends (effecting evolutionary homeostasis) or supplement them; its supplementary effect is probably increasingly important in the evolution of increasingly organized populations.

Darwin and sexual selection: One hundred years of misunderstanding.

PubMed

Veuille, Michel

2010-02-01

Darwin's book on the Descent of Man and Selection in Relation to Sex (1871) is often viewed as the continuation of The Origin of Species published 12 years earlier (1859), both because of the implicit parallelism between natural selection and sexual selection, and because Darwin himself presents the book as developing a subject (man) which he intentionally omitted in the Origin. But the Descent can also be viewed as the continuation of his book on Variation published three years earlier (1868). Firstly because Darwin's hypothesis of pangenesis links the selection process to the origin of variation through use and disuse, an idea underlying his speculations on the origin of moral sense in humans. Second because like the action of the horticulturist on his domestic crops, sexual selection exerted by one sex on the other sex can develop fancy traits that are not easily accounted for by their utility to the selected organism itself, such as artistic taste, pride, courage, and the morphological differences between human populations. These traits are difficult to reconcile with pangenesis. They add up to other contradictions of the book possibly resulting from Darwin's erroneous inference about the mechanism of inheritance, like those on the determination of sex-ratio, or the confusion between individual adaptation and the advantage to the species. These inconsistencies inaugurate a weakening of the Darwinian message, which will last 50 years after his death. They contributed to the neglect of sexual selection for a century. Darwin however maintained a logical distinction between evolutionary mechanisms and hereditary mechanisms, and an epistemological distinction between evolutionary theory and Pangenesis hypothesis. In the modern context of Mendelian genetics, Darwin's sexual selection retrospectively appears as luminous an idea in its pure principle as natural selection, even though the mechanisms governing the evolution of sexual choice in animals remain largely

Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease.

PubMed

Feinberg, Andrew P; Irizarry, Rafael A

2010-01-26

Neo-Darwinian evolutionary theory is based on exquisite selection of phenotypes caused by small genetic variations, which is the basis of quantitative trait contribution to phenotype and disease. Epigenetics is the study of nonsequence-based changes, such as DNA methylation, heritable during cell division. Previous attempts to incorporate epigenetics into evolutionary thinking have focused on Lamarckian inheritance, that is, environmentally directed epigenetic changes. Here, we propose a new non-Lamarckian theory for a role of epigenetics in evolution. We suggest that genetic variants that do not change the mean phenotype could change the variability of phenotype; and this could be mediated epigenetically. This inherited stochastic variation model would provide a mechanism to explain an epigenetic role of developmental biology in selectable phenotypic variation, as well as the largely unexplained heritable genetic variation underlying common complex disease. We provide two experimental results as proof of principle. The first result is direct evidence for stochastic epigenetic variation, identifying highly variably DNA-methylated regions in mouse and human liver and mouse brain, associated with development and morphogenesis. The second is a heritable genetic mechanism for variable methylation, namely the loss or gain of CpG dinucleotides over evolutionary time. Finally, we model genetically inherited stochastic variation in evolution, showing that it provides a powerful mechanism for evolutionary adaptation in changing environments that can be mediated epigenetically. These data suggest that genetically inherited propensity to phenotypic variability, even with no change in the mean phenotype, substantially increases fitness while increasing the disease susceptibility of a population with a changing environment.

Antibiotics and antibiotic resistance: a bitter fight against evolution.

PubMed

Rodríguez-Rojas, Alexandro; Rodríguez-Beltrán, Jerónimo; Couce, Alejandro; Blázquez, Jesús

2013-08-01

One of the most terrible consequences of Darwinian evolution is arguably the emergence and spread of antibiotic resistance, which is becoming a serious menace to modern societies. While spontaneous mutation, recombination and horizontal gene transfer are recognized as the main causes of this notorious phenomenon; recent research has raised awareness that sub-lethal concentrations of antibiotics can also foster resistance as an undesirable side-effect. They can produce genetic changes by different ways, including a raise of free radicals within the cell, induction of error-prone DNA-polymerases mediated by SOS response, imbalanced nucleotide metabolism or affect directly DNA. In addition to certain environmental conditions, subinhibitory concentrations of antimicrobials may increase, even more, the mutagenic effect of antibiotics. Here, we review the state of knowledge on antibiotics as promoters of antibiotic resistance. Copyright © 2013 Elsevier GmbH. All rights reserved.

An evolutionary framework for cultural change: Selectionism versus communal exchange

NASA Astrophysics Data System (ADS)

Gabora, Liane

2013-06-01

Dawkins' replicator-based conception of evolution has led to widespread mis-application of selectionism across the social sciences because it does not address the paradox that necessitated the theory of natural selection in the first place: how do organisms accumulate change when traits acquired over their lifetime are obliterated? This is addressed by von Neumann's concept of a self-replicating automaton (SRA). A SRA consists of a self-assembly code that is used in two distinct ways: (1) actively deciphered during development to construct a self-similar replicant, and (2) passively copied to the replicant to ensure that it can reproduce. Information that is acquired over a lifetime is not transmitted to offspring, whereas information that is inherited during copying is transmitted. In cultural evolution there is no mechanism for discarding acquired change. Acquired change can accumulate orders of magnitude faster than, and quickly overwhelm, inherited change due to differential replication of variants in response to selection. This prohibits a selectionist but not an evolutionary framework for culture and the creative processes that fuel it. The importance non-Darwinian processes in biological evolution is increasingly recognized. Recent work on the origin of life suggests that early life evolved through a non-Darwinian process referred to as communal exchange that does not involve a self-assembly code, and that natural selection emerged from this more haphazard, ancestral evolutionary process. It is proposed that communal exchange provides an evolutionary framework for culture that enables specification of cognitive features necessary for a (real or artificial) societies to evolve culture. This is supported by a computational model of cultural evolution and a conceptual network based program for documenting material cultural history, and it is consistent with high levels of human cooperation.

The sexual selection paradigm: have we overlooked other mechanisms in the evolution of male ornaments?

PubMed

Candolin, Ulrika; Tukiainen, Iina

2015-10-07

Extravagant male ornaments expressed during reproduction are almost invariably assumed to be sexually selected and evolve through competition for mating opportunities. Yet in species where male reproductive success depends on the defence of offspring, male ornaments could also evolve through social competition for offspring survival. However, in contrast to female ornaments, this possibility has received little attention in males. We show that a male ornament that is traditionally assumed to be sexually selected--the red nuptial coloration of the three-spined stickleback--is under stronger selection for offspring survival than for mating success. Males express most coloration during parenting, when they no longer attract females, and the colour correlates with nest retention and hatching success but not with attractiveness to females. This contradicts earlier assumptions and suggests that social selection for offspring survival rather than for sexual selection for mating success is the main mechanism maintaining the ornament in the population. These results suggest that we should consider other forms of social selection beyond sexual selection when seeking to explain the function and evolution of male ornaments. An incorrect assignment of selection pressures could hamper our understanding of evolution. © 2015 The Author(s).

The scope and strength of sex-specific selection in genome evolution.

PubMed

Wright, A E; Mank, J E

2013-09-01

Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Duplication and concerted evolution in a master sex determiner under balancing selection.

PubMed

Privman, Eyal; Wurm, Yannick; Keller, Laurent

2013-05-07

The transformer (tra) gene is a key regulator in the signalling hierarchy controlling all aspects of somatic sexual differentiation in Drosophila and other insects. Here, we show that six of the seven sequenced ants have two copies of tra. Surprisingly, the two paralogues are always more similar within species than among species. Comparative sequence analyses indicate that this pattern is owing to the ongoing concerted evolution after an ancestral duplication rather than independent duplications in each of the six species. In particular, there was strong support for inter-locus recombination between the paralogues of the ant Atta cephalotes. In the five species where the location of paralogues is known, they are adjacent to each other in four cases and separated by only few genes in the fifth case. Because there have been extensive genomic rearrangements in these lineages, this suggests selection acting to conserve their synteny. In three species, we also find a signature of positive selection in one of the paralogues. In three bee species where information is available, the tra gene is also duplicated, the copies are adjacent and in at least one species there was recombination between paralogues. These results suggest that concerted evolution plays an adaptive role in the evolution of this gene family.

Cultural selection drives the evolution of human communication systems

PubMed Central

Tamariz, Monica; Ellison, T. Mark; Barr, Dale J.; Fay, Nicolas

2014-01-01

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems. PMID:24966310

Cultural selection drives the evolution of human communication systems.

PubMed

Tamariz, Monica; Ellison, T Mark; Barr, Dale J; Fay, Nicolas

2014-08-07

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.

Evolution of female multiple mating: A quantitative model of the “sexually selected sperm” hypothesis

PubMed Central

Bocedi, Greta; Reid, Jane M

2015-01-01

Explaining the evolution and maintenance of polyandry remains a key challenge in evolutionary ecology. One appealing explanation is the sexually selected sperm (SSS) hypothesis, which proposes that polyandry evolves due to indirect selection stemming from positive genetic covariance with male fertilization efficiency, and hence with a male's success in postcopulatory competition for paternity. However, the SSS hypothesis relies on verbal analogy with “sexy-son” models explaining coevolution of female preferences for male displays, and explicit models that validate the basic SSS principle are surprisingly lacking. We developed analogous genetically explicit individual-based models describing the SSS and “sexy-son” processes. We show that the analogy between the two is only partly valid, such that the genetic correlation arising between polyandry and fertilization efficiency is generally smaller than that arising between preference and display, resulting in less reliable coevolution. Importantly, indirect selection was too weak to cause polyandry to evolve in the presence of negative direct selection. Negatively biased mutations on fertilization efficiency did not generally rescue runaway evolution of polyandry unless realized fertilization was highly skewed toward a single male, and coevolution was even weaker given random mating order effects on fertilization. Our models suggest that the SSS process is, on its own, unlikely to generally explain the evolution of polyandry. PMID:25330405

Relaxation of selection, niche construction, and the Baldwin effect in language evolution.

PubMed

Yamauchi, Hajime; Hashimoto, Takashi

2010-01-01

Deacon has suggested that one of the key factors of language evolution is not characterized by an increase in genetic contribution, often known as the Baldwin effect, but rather by a decrease. This process effectively increases linguistic learning capability by organizing a novel synergy of multiple lower-order functions previously irrelevant to the process of language acquisition. Deacon posits that this transition is not caused by natural selection. Rather, it is due to the relaxation of natural selection. While there are some cases in which relaxation caused by some external factors indeed induces the transition, we do not know what kind of relaxation has worked in language evolution. In this article, a genetic-algorithm-based computer simulation is used to investigate how the niche-constructing aspect of linguistic behavior may trigger the degradation of genetic predisposition related to language learning. The results show that agents initially increase their genetic predisposition for language learning—the Baldwin effect. They create a highly uniform sociolinguistic environment—a linguistic niche construction. This means that later generations constantly receive very similar inputs from adult agents, and subsequently the selective pressure to retain the genetic predisposition is relaxed.

Teaching Darwinian Evolution: Learning from Religious Education

ERIC Educational Resources Information Center

Stolberg, Tonie L.

2010-01-01

This article examines what science education might be able to learn from phenomenological religious education's attempts to teach classes where students hold a plurality of religious beliefs. Recent statements as to how best to accomplish the central pedagogical concept of "learning from religion" as a vehicle for human transformation are…

Models of protocellular structures, functions and evolution

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; New, Michael H.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The central step in the origin of life was the emergence of organized structures from organic molecules available on the early earth. These predecessors to modern cells, called 'proto-cells,' were simple, membrane bounded structures able to maintain themselves, grow, divide, and evolve. Since there is no fossil record of these earliest of life forms, it is a scientific challenge to discover plausible mechanisms for how these entities formed and functioned. To meet this challenge, it is essential to create laboratory models of protocells that capture the main attributes associated with living systems, while remaining consistent with known, or inferred, protobiological conditions. This report provides an overview of a project which has focused on protocellular metabolism and the coupling of metabolism to energy transduction. We have assumed that the emergence of systems endowed with genomes and capable of Darwinian evolution was preceded by a pre-genomic phase, in which protocells functioned and evolved using mostly proteins, without self-replicating nucleic acids such as RNA.

Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift.

PubMed

Johnson, Norman A; Porter, Adam H

2007-01-01

Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems.

PubMed

Acevedo-Rocha, Carlos G; Agudo, Ruben; Reetz, Manfred T

2014-12-10

Directed evolution of stereoselective enzymes provides a means to generate useful biocatalysts for asymmetric transformations in organic chemistry and biotechnology. Almost all of the numerous examples reported in the literature utilize high-throughput screening systems based on suitable analytical techniques. Since the screening step is the bottleneck of the overall procedure, researchers have considered the use of genetic selection systems as an alternative to screening. In principle, selection would be the most elegant and efficient approach because it is based on growth advantage of host cells harboring stereoselective mutants, but devising such selection systems is very challenging. They must be designed so that the host organism profits from the presence of an enantioselective variant. Progress in this intriguing research area is summarized in this review, which also includes some examples of display systems designed for enantioselectivity as assayed by fluorescence-activated cell sorting (FACS). Although the combination of display systems and FACS is a powerful approach, we also envision innovative ideas combining metabolic engineering and genetic selection systems with protein directed evolution for the development of highly selective and efficient biocatalysts. Copyright © 2014 Elsevier B.V. All rights reserved.

Evolution and selection of river networks: Statics, dynamics, and complexity

PubMed Central

Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R.; Maritan, Amos; Rodriguez-Iturbe, Ignacio

2014-01-01

Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept. PMID:24550264

Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

PubMed Central

McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801

Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae).

PubMed

McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

Quantifying Selective Pressures Driving Bacterial Evolution Using Lineage Analysis

NASA Astrophysics Data System (ADS)

Lambert, Guillaume; Kussell, Edo

2015-01-01

Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population's rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages—i.e., the life histories of individuals and their ancestors—to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to Escherichia coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems.

Quantifying selective pressures driving bacterial evolution using lineage analysis

PubMed Central

Lambert, Guillaume; Kussell, Edo

2015-01-01

Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population’s rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages –i.e. the life-histories of individuals and their ancestors– to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to E. coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life-history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection, and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems. PMID:26213639

A Cross-disciplinary Framework for the Description of Contextually Mediated Change

NASA Astrophysics Data System (ADS)

Gabora, Liane; Aerts, Diederik

We present a mathematical framework (referred to as Context-driven Actualization of Potential, or CAP) for describing how entities change over time under the influence of a context. The approach facilitates comparison of change of state of entities studied in different disciplines. Processes are seen to differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. Our analysis suggests that the dynamical evolution of a quantum entity described by the Schrödinger equation is not fundamentally different from change provoked by a measurement often referred to as collapse but a limiting case, with only one way to collapse. The biological transition to coded replication is seen as a means of preserving structure in the face of context, and sexual replication as a means of increasing potentiality thus enhancing diversity through interaction with context. The framework sheds light on concepts like selection and fitness, reveals how exceptional Darwinian evolution is as a means of 'change of state', and clarifies in what sense culture (and the creative process underlying it) are Darwinian.

Evolution of sex: Using experimental genomics to select among competing theories.

PubMed

Sharp, Nathaniel P; Otto, Sarah P

2016-08-01

Few topics have intrigued biologists as much as the evolution of sex. Understanding why sex persists despite its costs requires not just rigorous theoretical study, but also empirical data on related fundamental issues, including the nature of genetic variance for fitness, patterns of genetic interactions, and the dynamics of adaptation. The increasing feasibility of examining genomes in an experimental context is now shedding new light on these problems. Using this approach, McDonald et al. recently demonstrated that sex uncouples beneficial and deleterious mutations, allowing selection to proceed more effectively with sex than without. Here we discuss the insights provided by this study, along with other recent empirical work, in the context of the major theoretical models for the evolution of sex. © 2016 WILEY Periodicals, Inc.

Relaxation of herbivore-mediated selection drives the evolution of genetic covariances between plant competitive and defense traits.

PubMed

Uesugi, Akane; Connallon, Tim; Kessler, André; Monro, Keyne

2017-06-01

Insect herbivores are important mediators of selection on traits that impact plant defense against herbivory and competitive ability. Although recent experiments demonstrate a central role for herbivory in driving rapid evolution of defense and competition-mediating traits, whether and how herbivory shapes heritable variation in these traits remains poorly understood. Here, we evaluate the structure and evolutionary stability of the G matrix for plant metabolites that are involved in defense and allelopathy in the tall goldenrod, Solidago altissima. We show that G has evolutionarily diverged between experimentally replicated populations that evolved in the presence versus the absence of ambient herbivory, providing direct evidence for the evolution of G by natural selection. Specifically, evolution in an herbivore-free habitat altered the orientation of G, revealing a negative genetic covariation between defense- and competition-related metabolites that is typically masked in herbivore-exposed populations. Our results may be explained by predictions of classical quantitative genetic theory, as well as the theory of acquisition-allocation trade-offs. The study provides compelling evidence that herbivory drives the evolution of plant genetic architecture. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolution of resistance to a multiple-herbivore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection.

PubMed

Wise, Michael J; Rausher, Mark D

2013-06-01

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities-particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Frequency-dependent selection can lead to evolution of high mutation rates.

PubMed

Rosenbloom, Daniel I S; Allen, Benjamin

2014-05-01

Theoretical and experimental studies have shown that high mutation rates can be advantageous, especially in novel or fluctuating environments. Here we examine how frequency-dependent competition may lead to fluctuations in trait frequencies that exert upward selective pressure on mutation rates. We use a mathematical model to show that cyclical trait dynamics generated by "rock-paper-scissors" competition can cause the mutation rate in a population to converge to a high evolutionarily stable mutation rate, reflecting a trade-off between generating novelty and reproducing past success. Introducing recombination lowers the evolutionarily stable mutation rate but allows stable coexistence between mutation rates above and below the evolutionarily stable rate. Even considering strong mutational load and ignoring the costs of faithful replication, evolution favors positive mutation rates if the selective advantage of prevailing in competition exceeds the ratio of recombining to nonrecombining offspring. We discuss a number of genomic mechanisms that may meet our theoretical requirements for the adaptive evolution of mutation. Overall, our results suggest that local mutation rates may be higher on genes influencing cyclical competition and that global mutation rates in asexual species may be higher in populations subject to strong cyclical competition.

Darwin-Wallace Demons: survival of the fastest in populations of duckweeds and the evolutionary history of an enigmatic group of angiosperms.

PubMed

Kutschera, U; Niklas, K J

2015-01-01

In evolutionary biology, the term 'Darwinian fitness' refers to the lifetime reproductive success of an individual within a population of conspecifics. The idea of a 'Darwinian Demon' emerged from this concept and is defined here as an organism that commences reproduction almost immediately after birth, has a maximum fitness, and lives forever. It has been argued that duckweeds (sub-family Lemnoideae, order Alismatales), a group containing five genera and 34 species of small aquatic monocotyledonous plants with a reduced body plan, can be interpreted as examples of 'Darwinian Demons'. Here we focus on the species Spirodela polyrhiza (Great duckweed) and show that these miniaturised aquatic angiosperms display features that fit the definition of the hypothetical organism that we will call a 'Darwin-Wallace Demon' in recognition of the duel proponents of evolution by natural selection. A quantitative analysis (log-log bivariate plot of annual growth in dry biomass versus standing dry body mass of various green algae and land plants) revealed that duckweeds are thus far the most rapidly growing angiosperms in proportion to their body mass. In light of this finding, we discuss the disposable soma and metabolic optimising theories, summarise evidence for and against the proposition that the Lemnoideae (family Araceae) reflect an example of reductive evolution, and argue that, under real-world conditions (environmental constraints and other limitations), 'Darwin-Wallace Demons' cannot exist, although the concept remains useful in much the same way that the Hardy-Weinberg law does. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Divergent evolution of life span associated with mitochondrial DNA evolution.

PubMed

Stojković, Biljana; Sayadi, Ahmed; Đorđević, Mirko; Jović, Jelena; Savković, Uroš; Arnqvist, Göran

2017-01-01

Mitochondria play a key role in ageing. The pursuit of genes that regulate variation in life span and ageing have shown that several nuclear-encoded mitochondrial genes are important. However, the role of mitochondrial encoded genes (mtDNA) is more controversial and our appreciation of the role of mtDNA for the evolution of life span is limited. We use replicated lines of seed beetles that have been artificially selected for long or short life for >190 generations, now showing dramatic phenotypic differences, to test for a possible role of mtDNA in the divergent evolution of ageing and life span. We show that these divergent selection regimes led to the evolution of significantly different mtDNA haplotype frequencies. Selection for a long life and late reproduction generated positive selection for one specific haplotype, which was fixed in most such lines. In contrast, selection for reproduction early in life led to both positive selection as well as negative frequency-dependent selection on two different haplotypes, which were both present in all such lines. Our findings suggest that the evolution of life span was in part mediated by mtDNA, providing support for the emerging general tenet that adaptive evolution of life-history syndromes may involve mtDNA. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

The Roles of Sexual and Viability Selection in the Evolution of Incomplete Reproductive Isolation: From Allopatry to Sympatry.

PubMed

Cotto, Olivier; Servedio, Maria R

2017-11-01

In recent years, theoretical models have introduced the concept that ongoing hybridization between "good" species can occur because incomplete reproductive isolation can be a selected optimum. They furthermore show that positive frequency-dependent sexual selection, which is naturally generated by some of the underlying processes that lead to assortative mating, plays a key role in the evolution of incomplete reproductive isolation. This occurs, however, through different mechanisms in sympatric versus allopatric scenarios. We investigate the evolution of incomplete reproductive isolation by sexual selection in scenarios ranging from sympatry to allopatry, to examine how these mechanisms interact. We consider an ecological scenario in which there are two habitats used during foraging and individuals can breed either within a habitat or in a common mating pool. We find that when trait divergence is maintained, sexual selection drives the evolution of choosiness in opposite ways in the common mating pool versus within each habitat. Specifically, strong choosiness is favored in the common mating pool, whereas intermediate choosiness is favored within habitat; the interaction of these forces determines whether intermediate reproductive isolation ultimately evolves in the system. We further find cases where the evolution of stronger choosiness occurs but leads to the loss of divergence. Overall, our study shows that contrasting forces on the evolution of reproductive isolation can occur in different mating areas, and we propose a new avenue for understanding the diversity in levels of reproductive isolation within and across species.

Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection.

PubMed

Huang, Huateng; Rabosky, Daniel L

2015-09-16

Sexual dichromatism is the tendency for sexes to differ in color pattern and represents a striking form of within-species morphological variation. Conspicuous intersexual differences in avian plumage are generally thought to result from Darwinian sexual selection, to the extent that dichromatism is often treated as a surrogate for the intensity of sexual selection in phylogenetic comparative studies. Intense sexual selection is predicted to leave a footprint on genetic evolution by reducing the relative genetic diversity on sex chromosome to that on the autosomes. In this study, we test the association between plumage dichromatism and sex-linked genetic diversity using eight species pairs with contrasting levels of dichromatism. We estimated Z-linked and autosomal genetic diversity for these non-model avian species using restriction-site associated (RAD) loci that covered ~3 % of the genome. We find that monochromatic birds consistently have reduced sex-linked genomic variation relative to phylogenetically-paired dichromatic species and this pattern is robust to mutational biases. Our results are consistent with several interpretations. If present-day sexual selection is stronger in dichromatic birds, our results suggest that its impact on sex-linked genomic variation is offset by other processes that lead to proportionately lower Z-linked variation in monochromatic species. We discuss possible factors that may contribute to this discrepancy between phenotypes and genomic variation. Conversely, it is possible that present-day sexual selection -- as measured by the variance in male reproductive success -- is stronger in the set of monochromatic taxa we have examined, potentially reflecting the importance of song, behavior and other non-plumage associated traits as targets of sexual selection. This counterintuitive finding suggests that the relationship between genomic variation and sexual selection is complex and highlights the need for a more comprehensive survey

Signal design and perception in Hypocnemis antbirds: evidence for convergent evolution via social selection.

PubMed

Tobias, Joseph A; Seddon, Nathalie

2009-12-01

Natural selection is known to produce convergent phenotypes through mimicry or ecological adaptation. It has also been proposed that social selection--i.e., selection exerted by social competition--may drive convergent evolution in signals mediating interspecific communication, yet this idea remains controversial. Here, we use color spectrophotometry, acoustic analyses, and playback experiments to assess the hypothesis of adaptive signal convergence in two competing nonsister taxa, Hypocnemis peruviana and H. subflava (Aves: Thamnophilidae). We show that the structure of territorial songs in males overlaps in sympatry, with some evidence of convergent character displacement. Conversely, nonterritorial vocal and visual signals in males are strikingly diagnostic, in line with 6.8% divergence in mtDNA sequences. The same pattern of variation applies to females. Finally, we show that songs in both sexes elicit strong territorial responses within and between species, whereas songs of a third, allopatric and more closely related species (H. striata) are structurally divergent and elicit weaker responses. Taken together, our results provide compelling evidence that social selection can act across species boundaries to drive convergent or parallel evolution in taxa competing for space and resources.

Joint evolution of multiple social traits: a kin selection analysis

PubMed Central

Brown, Sam P.; Taylor, Peter D.

2010-01-01

General models of the evolution of cooperation, altruism and other social behaviours have focused almost entirely on single traits, whereas it is clear that social traits commonly interact. We develop a general kin-selection framework for the evolution of social behaviours in multiple dimensions. We show that whenever there are interactions among social traits new behaviours can emerge that are not predicted by one-dimensional analyses. For example, a prohibitively costly cooperative trait can ultimately be favoured owing to initial evolution in other (cheaper) social traits that in turn change the cost–benefit ratio of the original trait. To understand these behaviours, we use a two-dimensional stability criterion that can be viewed as an extension of Hamilton's rule. Our principal example is the social dilemma posed by, first, the construction and, second, the exploitation of a shared public good. We find that, contrary to the separate one-dimensional analyses, evolutionary feedback between the two traits can cause an increase in the equilibrium level of selfish exploitation with increasing relatedness, while both social (production plus exploitation) and asocial (neither) strategies can be locally stable. Our results demonstrate the importance of emergent stability properties of multidimensional social dilemmas, as one-dimensional stability in all component dimensions can conceal multidimensional instability. PMID:19828549

Evolution Stings: The Origin and Diversification of Scorpion Toxin Peptide Scaffolds

PubMed Central

Sunagar, Kartik; Undheim, Eivind A. B.; Chan, Angelo H. C.; Koludarov, Ivan; Muñoz-Gómez, Sergio A.; Antunes, Agostinho; Fry, Bryan G.

2013-01-01

The episodic nature of natural selection and the accumulation of extreme sequence divergence in venom-encoding genes over long periods of evolutionary time can obscure the signature of positive Darwinian selection. Recognition of the true biocomplexity is further hampered by the limited taxon selection, with easy to obtain or medically important species typically being the subject of intense venom research, relative to the actual taxonomical diversity in nature. This holds true for scorpions, which are one of the most ancient terrestrial venomous animal lineages. The family Buthidae that includes all the medically significant species has been intensely investigated around the globe, while almost completely ignoring the remaining non-buthid families. Australian scorpion lineages, for instance, have been completely neglected, with only a single scorpion species (Urodacus yaschenkoi) having its venom transcriptome sequenced. Hence, the lack of venom composition and toxin sequence information from an entire continent’s worth of scorpions has impeded our understanding of the molecular evolution of scorpion venom. The molecular origin, phylogenetic relationships and evolutionary histories of most scorpion toxin scaffolds remain enigmatic. In this study, we have sequenced venom gland transcriptomes of a wide taxonomical diversity of scorpions from Australia, including buthid and non-buthid representatives. Using state-of-art molecular evolutionary analyses, we show that a majority of CSα/β toxin scaffolds have experienced episodic influence of positive selection, while most non-CSα/β linear toxins evolve under the extreme influence of negative selection. For the first time, we have unraveled the molecular origin of the major scorpion toxin scaffolds, such as scorpion venom single von Willebrand factor C-domain peptides (SV-SVC), inhibitor cystine knot (ICK), disulphide-directed beta-hairpin (DDH), bradykinin potentiating peptides (BPP), linear non-disulphide bridged

Evolution stings: the origin and diversification of scorpion toxin peptide scaffolds.

PubMed

Sunagar, Kartik; Undheim, Eivind A B; Chan, Angelo H C; Koludarov, Ivan; Muñoz-Gómez, Sergio A; Antunes, Agostinho; Fry, Bryan G

2013-12-13

The episodic nature of natural selection and the accumulation of extreme sequence divergence in venom-encoding genes over long periods of evolutionary time can obscure the signature of positive Darwinian selection. Recognition of the true biocomplexity is further hampered by the limited taxon selection, with easy to obtain or medically important species typically being the subject of intense venom research, relative to the actual taxonomical diversity in nature. This holds true for scorpions, which are one of the most ancient terrestrial venomous animal lineages. The family Buthidae that includes all the medically significant species has been intensely investigated around the globe, while almost completely ignoring the remaining non-buthid families. Australian scorpion lineages, for instance, have been completely neglected, with only a single scorpion species (Urodacus yaschenkoi) having its venom transcriptome sequenced. Hence, the lack of venom composition and toxin sequence information from an entire continent's worth of scorpions has impeded our understanding of the molecular evolution of scorpion venom. The molecular origin, phylogenetic relationships and evolutionary histories of most scorpion toxin scaffolds remain enigmatic. In this study, we have sequenced venom gland transcriptomes of a wide taxonomical diversity of scorpions from Australia, including buthid and non-buthid representatives. Using state-of-art molecular evolutionary analyses, we show that a majority of CSα/β toxin scaffolds have experienced episodic influence of positive selection, while most non-CSα/β linear toxins evolve under the extreme influence of negative selection. For the first time, we have unraveled the molecular origin of the major scorpion toxin scaffolds, such as scorpion venom single von Willebrand factor C-domain peptides (SV-SVC), inhibitor cystine knot (ICK), disulphide-directed beta-hairpin (DDH), bradykinin potentiating peptides (BPP), linear non-disulphide bridged

The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups

PubMed Central

2013-01-01

Background WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species. Results We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean. Conclusions In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have

The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups.

PubMed

Yin, Guangjun; Xu, Hongliang; Xiao, Shuyang; Qin, Yajuan; Li, Yaxuan; Yan, Yueming; Hu, Yingkao

2013-10-03

WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species. We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean. In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have different evolutionary rates

Evolution of learning and levels of selection: A lesson from avian parent-offspring communication.

PubMed

Lotem, Arnon; Biran-Yoeli, Inbar

2013-09-20

In recent years, it has become increasingly clear that the evolution of behavior may be better understood as the evolution of the learning mechanisms that produce it, and that such mechanisms should be modeled and tested explicitly. However, this approach, which has recently been applied to animal foraging and decision-making, has rarely been applied to the social and communicative behaviors that are likely to operate in complex social environments and be subject to multi-level selection. Here we use genetic, agent-based evolutionary simulations to explore how learning mechanisms may evolve to adjust the level of nestling begging (offspring signaling of need), and to examine the possible consequences of this process for parent-offspring conflict and communication. In doing so, we also provide the first step-by-step dynamic model of parent-offspring communication. The results confirm several previous theoretical predictions and demonstrate three novel phenomena. First, negatively frequency-dependent group-level selection can generate a stable polymorphism of learning strategies and parental responses. Second, while conventional reinforcement learning models fail to cope successfully with family dynamics at the nest, a newly developed learning model (incorporating behaviors that are consistent with recent experimental results on learning in nestling begging) produced effective learning, which evolved successfully. Third, while kin-selection affects the frequency of the different learning genes, its impact on begging slope and intensity was unexpectedly negligible, demonstrating that evolution is a complex process, and showing that the effect of kin-selection on behaviors that are shaped by learning may not be predicted by simple application of Hamilton's rule. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolution of learning and levels of selection: a lesson from avian parent-offspring communication.

PubMed

Lotem, Arnon; Biran-Yoeli, Inbar

2014-02-01

In recent years, it has become increasingly clear that the evolution of behavior may be better understood as the evolution of the learning mechanisms that produce it, and that such mechanisms should be modeled and tested explicitly. However, this approach, which has recently been applied to animal foraging and decision-making, has rarely been applied to the social and communicative behaviors that are likely to operate in complex social environments and be subject to multi-level selection. Here we use genetic, agent-based evolutionary simulations to explore how learning mechanisms may evolve to adjust the level of nestling begging (offspring signaling of need), and to examine the possible consequences of this process for parent-offspring conflict and communication. In doing so, we also provide the first step-by-step dynamic model of parent-offspring communication. The results confirm several previous theoretical predictions and demonstrate three novel phenomena. First, negatively frequency-dependent group-level selection can generate a stable polymorphism of learning strategies and parental responses. Second, while conventional reinforcement learning models fail to cope successfully with family dynamics at the nest, a newly developed learning model (incorporating behaviors that are consistent with recent experimental results on learning in nestling begging) produced effective learning, which evolved successfully. Third, while kin-selection affects the frequency of the different learning genes, its impact on begging slope and intensity was unexpectedly negligible, demonstrating that evolution is a complex process, and showing that the effect of kin-selection on behaviors that are shaped by learning may not be predicted by simple application of Hamilton's rule. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolution of Site-Selection Stabilizes Population Dynamics, Promotes Even Distribution of Individuals, and Occasionally Causes Evolutionary Suicide.

PubMed

Parvinen, Kalle; Brännström, Åke

2016-08-01

Species that compete for access to or use of sites, such as parasitic mites attaching to honey bees or apple maggots laying eggs in fruits, can potentially increase their fitness by carefully selecting sites at which they face little or no competition. Here, we systematically investigate the evolution of site-selection strategies among animals competing for discrete sites. By developing and analyzing a mechanistic and population-dynamical model of site selection in which searching individuals encounter sites sequentially and can choose to accept or continue to search based on how many conspecifics are already there, we give a complete characterization of the different site-selection strategies that can evolve. We find that evolution of site-selection stabilizes population dynamics, promotes even distribution of individuals among sites, and occasionally causes evolutionary suicide. We also discuss the broader implications of our findings and propose how they can be reconciled with an earlier study (Nonaka et al. in J Theor Biol 317:96-104, 2013) that reported selection toward ever higher levels of aggregation among sites as a consequence of site-selection.

A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus).

PubMed

Chapman, Mark A; Pashley, Catherine H; Wenzler, Jessica; Hvala, John; Tang, Shunxue; Knapp, Steven J; Burke, John M

2008-11-01

Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues as to the roles that these genes may have played during sunflower evolution.

Molecular evolution of the ependymin protein family: a necessary update.

PubMed

Suárez-Castillo, Edna C; García-Arrarás, José E

2007-02-15

Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified in other vertebrates, including amphibians and mammals. Recently, we reported the identification and characterization of an Epdr in echinoderms, showing that there are ependymin family members in non-vertebrate deuterostomes. We have now explored multiple databases to find Epdrs in different metazoan species. Using these sequences we have performed genome mapping, molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship among ependymin proteins. Our results demonstrate that ependymin genes are also present in protostomes. In addition, as a result of the putative fish-specific genome duplication event and posterior divergence, the ependymin family can be divided into four groups according to their amino acid composition and branching pattern in the gene tree: 1) a brain-specific group of ependymin sequences that is unique to teleost fishes and encompasses the originally described ependymin; 2) a group expressed in non-brain tissue in fishes; 3) a group expressed in several tissues that appears to be deuterostome-specific, and 4) a group found in invertebrate deuterostomes and protostomes, with a broad pattern of expression and that probably represents the evolutionary origin of the ependymins. Using codon-substitution models to statistically assess the selective pressures acting over the ependymin protein family, we found evidence of episodic positive Darwinian selection and relaxed selective constraints in each one of the postduplication branches of the gene tree. However, purifying selection (with among-site variability) appears to be the main influence on the evolution of each subgroup within the family. Functional divergence among the ependymin paralog

Evolving Better Cars: Teaching Evolution by Natural Selection with a Digital Inquiry Activity

ERIC Educational Resources Information Center

Royer, Anne M.; Schultheis, Elizabeth H.

2014-01-01

Evolutionary experiments are usually difficult to perform in the classroom because of the large sizes and long timescales of experiments testing evolutionary hypotheses. Computer applications give students a window to observe evolution in action, allowing them to gain comfort with the process of natural selection and facilitating inquiry…

Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.

PubMed

Hodgins, Kathryn A; Yeaman, Sam; Nurkowski, Kristin A; Rieseberg, Loren H; Aitken, Sally N

2016-06-01

The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Using theories of sexual selection and sexual conflict to improve our understanding of plant ecology and evolution

PubMed Central

Lankinen, Åsa; Karlsson Green, Kristina

2015-01-01

Today it is accepted that the theories of sexual selection and sexual conflict are general and can be applied to both animals and plants. However, potentially due to a controversial history, plant studies investigating sexual selection and sexual conflict are relatively rare. Moreover, these theories and concepts are seldom implemented in research fields investigating related aspects of plant ecology and evolution. Even though these theories are complex, and can be difficult to study, we suggest that several fields in plant biology would benefit from incorporating and testing the impact of selection pressures generated by sexual selection and sexual conflict. Here we give examples of three fields where we believe such incorporation would be particularly fruitful, including (i) mechanisms of pollen–pistil interactions, (ii) mating-system evolution in hermaphrodites and (iii) plant immune responses to pests and pathogens. PMID:25613227

Continuous and discontinuous phase transitions in the evolution of a polygenic trait under stabilizing selective pressure

NASA Astrophysics Data System (ADS)

Fierro, Annalisa; Cocozza, Sergio; Monticelli, Antonella; Scala, Giovanni; Miele, Gennaro

2017-06-01

The presence of phenomena analogous to phase transition in Statistical Mechanics has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model system, we analyze the evolution of a population of N diploid hermaphrodites in random mating regime. The population evolves under the effect of drift, selective pressure in form of viability on an additive polygenic trait, and mutation. The analysis allows to determine a phase diagram in the plane of mutation rate and strength of selection. The involved pattern of phase transitions is characterized by a line of critical points for weak selective pressure (smaller than a threshold), whereas discontinuous phase transitions, characterized by metastable hysteresis, are observed for strong selective pressure. A finite-size scaling analysis suggests the analogy between our system and the mean-field Ising model for selective pressure approaching the threshold from weaker values. In this framework, the mutation rate, which allows the system to explore the accessible microscopic states, is the parameter controlling the transition from large heterozygosity ( disordered phase) to small heterozygosity ( ordered one).

The Evolution of Massive Stars: a Selection of Facts and Questions

NASA Astrophysics Data System (ADS)

Vanbeveren, D.

In the present paper we discuss a selection of facts and questions related to observations and evolutionary calculations of massive single stars and massive stars in interacting binaries. We focus on the surface chemical abundances, the role of stellar winds, the early Be-stars, the high mass X-ray binaries and the effects of rotation on stellar evolution. Finally, we present an unconventionally formed object scenario (UFO-scenario) of WR binaries in dense stellar environments.

EVOLUTION OF DIVERGENT FEMALE MATING PREFERENCE IN RESPONSE TO EXPERIMENTAL SEXUAL SELECTION

PubMed Central

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-01-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. PMID:24931497

Explanation of climate and human impacts on sediment discharge change in Darwinian hydrology: Derivation of a differential equation

NASA Astrophysics Data System (ADS)

Zhang, Jianjun; Gao, Guangyao; Fu, Bojie; Zhang, Lu

2018-04-01

The assessment for impacts of climate variability and human activities on suspended sediment yield (SSY) change has long been a question of great interest. However, the sediment generation processes are sophisticated with high nonlinearity and great uncertainty, which give rise to extreme complexity for SSY change assessment in Newtonian approach. Consequently, few approaches can be simply but widely applied to decompose impacts of climatic variability and human activities on SSY change. Thus, it is an urgent need to develop advanced methods that are simple and robust. Since that the Newtonian approach is hardly achievable due to limitation of either observations or knowledge of mechanisms, there have been repeated calls to capture the hydrologic system in Darwinian approach for hydrological change prediction or explanation. As streamflow is the carrier of suspended sediment, SSY change are thus documented in changes of sediment concentrated flow and suspended sediment concentration - water discharge (C-Q) relationships. By deduced corollaries, a differential equation of sediment discharge change was derived to explicitly decompose impacts of climate variability and human activities in Darwinian hydrology. Besides, a new form of sediment rating curves was proposed and curved as C-Q relationships and probability distribution of sediment concentrated flow. River sediment flux can be revealed by this representation, which simply elucidates mechanism of SSY generation covering a range of time scales from finer than rainfall-event to long term. By the new sediment rating curves, the differential equation was partly solved using a segmentation algorithm proposed and validated in this paper, and then was submitted to water balance framework expressed by Budyko-type equation. Thus, for catchment management, hydrologists can obtain explicit explanation of how climate variation and human activities propagate through landscape and result in sediment discharge change. The

The evolution of episodic memory

PubMed Central

Allen, Timothy A.; Fortin, Norbert J.

2013-01-01

One prominent view holds that episodic memory emerged recently in humans and lacks a “(neo)Darwinian evolution” [Tulving E (2002) Annu Rev Psychol 53:1–25]. Here, we review evidence supporting the alternative perspective that episodic memory has a long evolutionary history. We show that fundamental features of episodic memory capacity are present in mammals and birds and that the major brain regions responsible for episodic memory in humans have anatomical and functional homologs in other species. We propose that episodic memory capacity depends on a fundamental neural circuit that is similar across mammalian and avian species, suggesting that protoepisodic memory systems exist across amniotes and, possibly, all vertebrates. The implication is that episodic memory in diverse species may primarily be due to a shared underlying neural ancestry, rather than the result of evolutionary convergence. We also discuss potential advantages that episodic memory may offer, as well as species-specific divergences that have developed on top of the fundamental episodic memory architecture. We conclude by identifying possible time points for the emergence of episodic memory in evolution, to help guide further research in this area. PMID:23754432

Brain size evolution in pipefishes and seahorses: the role of feeding ecology, life history and sexual selection.

PubMed

Tsuboi, M; Lim, A C O; Ooi, B L; Yip, M Y; Chong, V C; Ahnesjö, I; Kolm, N

2017-01-01

Brain size varies greatly at all taxonomic levels. Feeding ecology, life history and sexual selection have been proposed as key components in generating contemporary diversity in brain size across vertebrates. Analyses of brain size evolution have, however, been limited to lineages where males predominantly compete for mating and females choose mates. Here, we present the first original data set of brain sizes in pipefishes and seahorses (Syngnathidae) a group in which intense female mating competition occurs in many species. After controlling for the effect of shared ancestry and overall body size, brain size was positively correlated with relative snout length. Moreover, we found that females, on average, had 4.3% heavier brains than males and that polyandrous species demonstrated more pronounced (11.7%) female-biased brain size dimorphism. Our results suggest that adaptations for feeding on mobile prey items and sexual selection in females are important factors in brain size evolution of pipefishes and seahorses. Most importantly, our study supports the idea that sexual selection plays a major role in brain size evolution, regardless of on which sex sexual selection acts stronger. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolution of DMY, a newly emergent male sex-determination gene of medaka fish.

PubMed

Zhang, Jianzhi

2004-04-01

The Japanese medaka fish Oryzias latipes has an XX/XY sex-determination system. The Y-linked sex-determination gene DMY is a duplicate of the autosomal gene DMRT1, which encodes a DM-domain-containing transcriptional factor. DMY appears to have originated recently within Oryzias, allowing a detailed evolutionary study of the initial steps that led to the new gene and new sex-determination system. Here I analyze the publicly available DMRT1 and DMY gene sequences of Oryzias species and report the following findings. First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, consistent with the male-driven evolution hypothesis. Second, the ratio of the rate of nonsynonymous nucleotide substitution (d(N)) to that of synonymous substitution (d(S)) is significantly higher in DMY than in DMRT1. Third, in DMRT1, the d(N)/d(S) ratio for the DM domain is lower than that for non-DM regions, as expected from the functional importance of the DM domain. But in DMY, the opposite is observed and the DM domain is likely under positive Darwinian selection. Fourth, only one characteristic amino acid distinguishes all DMY sequences from all DMRT1 sequences, suggesting that a single amino acid change may be largely responsible for the establishment of DMY as the male sex-determination gene in medaka fish.

Convergent evolution and divergent selection: lizards at the White Sands ecotone.

PubMed

Rosenblum, Erica Bree

2006-01-01

Ecological transition zones, where organismal phenotypes result from a delicate balance between selection and migration, highlight the interplay of local adaptation and gene flow. Here, I study the response of an entire species assemblage to natural selection across a common ecotone. Three lizard species, distributed along a dramatic environmental gradient in substrate color, display convergent adaptation of blanched coloration on the gypsum dunes of White Sands National Monument. I investigate the role of gene flow in modulating phenotypic response to selection by quantifying color variation and genetic variation across the ecotone. I find species differences in degree of background matching and in genetic connectivity of populations across the ecotone. Differences among species in phenotypic response to selection scale precisely to levels of genetic isolation. Species with higher levels of gene flow across the ecotone exhibit less dramatic responses to selection. Results also reveal a strong signal of ecologically mediated divergence for White Sands lizards. For all species, phenotypic variation is better explained by habitat similarity than genetic similarity. Convergent evolution of blanched coloration at White Sands clearly reflects the action of strong divergent selection; however, adaptive response appears to be modulated by gene flow and demographic history and can be predicted by divergence-with-gene-flow models.

Constructor theory of life

PubMed Central

Marletto, Chiara

2015-01-01

Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection. In this paper, I show that for those processes to be possible without the design of biological adaptations being encoded in the laws of physics, those laws must have certain other properties. The theory of what these properties are is not part of evolution theory proper, yet without it the neo-Darwinian theory does not fully achieve its purpose of explaining the appearance of design. To this end, I apply constructor theory's new mode of explanation to express exactly within physics the appearance of design, no-design laws, and the logic of self-reproduction and natural selection. I conclude that self-reproduction, replication and natural selection are possible under no-design laws, the only non-trivial condition being that they allow digital information to be physically instantiated. This has an exact characterization in the constructor theory of information. I also show that under no-design laws an accurate replicator requires the existence of a ‘vehicle’ constituting, together with the replicator, a self-reproducer. PMID:25589566

Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family.

PubMed

Li, Gang; Janecka, Jan E; Murphy, William J

2011-02-01

Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evolution of pheromone-based communication, recognition, and mate selection in wild animals. We sequenced the gene encoding cauxin, CES7, in 22 species representing all major felid lineages, and multiple outgroups and showed that it has undergone rapid evolutionary change preceding and during the diversification of the cat family. A comparison between feline cauxin and orthologous carboxylesterases from other mammalian lineages revealed evidence of strong positive Darwinian selection within and between several cat lineages, enriched at functionally important sites of the protein. The higher rate of radical amino acid replacements in small felids, coupled with the lack of felinine and extremely low levels of cauxin in the urine of the great cats (Panthera), correlates with functional divergence of this gene in Panthera, and its putative loss in the snow leopard. Expression studies found evidence for several alternatively spliced transcripts in testis and brain, suggesting additional roles in male reproductive fitness and behavior. Our work presents the first report of strong positive natural selection acting on a major urinary protein of nonrodent mammals, providing evidence for parallel selection pressure on the regulation of pheromones in different mammalian lineages, despite the use of different metabolic pathways. Our results imply that natural selection may drive rapid changes in the regulation of pheromones in urine among the different cat species, which in turn may influence social behavior, such as territorial marking and conspecific recognition, therefore serving as an important mechanism for the radiation of this group

Hormones and the Evolution of Complex Traits: Insights from Artificial Selection on Behavior

PubMed Central

Garland, Theodore; Zhao, Meng; Saltzman, Wendy

2016-01-01

Although behavior may often be a fairly direct target of natural or sexual selection, it cannot evolve without changes in subordinate traits that cause or permit its expression. In principle, changes in endocrine function could be a common mechanism underlying behavioral evolution because they are well positioned to mediate integrated responses to behavioral selection. More specifically, hormones can influence both motivational (e.g., brain) and performance (e.g., muscles) components of behavior simultaneously and in a coordinated fashion. If the endocrine system is often “used” as a general mechanism to effect responses to selection, then correlated responses in other aspects of behavior, life history, and organismal performance (e.g., locomotor abilities) should commonly occur because any cell with appropriate receptors could be affected. Ways in which behavior coadapts with other aspects of the phenotype can be studied directly through artificial selection and experimental evolution. Several studies have targeted rodent behavior for selective breeding and reported changes in other aspects of behavior, life history, and lower-level effectors of these organismal traits, including endocrine function. One example involves selection for high levels of voluntary wheel running, one aspect of physical activity, in four replicate High Runner (HR) lines of mice. Circulating levels of several hormones (including insulin, testosterone, thyroxine, triiodothyronine) have been characterized, three of which—corticosterone, leptin, and adiponectin—differ between HR and control lines, depending on sex, age, and generation. Potential changes in circulating levels of other behaviorally and metabolically relevant hormones, as well as in other components of the endocrine system (e.g., receptors), have yet to be examined. Overall, results to date identify promising avenues for further studies on the endocrine basis of activity levels. PMID:27252193

Hormones and the Evolution of Complex Traits: Insights from Artificial Selection on Behavior.

PubMed

Garland, Theodore; Zhao, Meng; Saltzman, Wendy

2016-08-01

Although behavior may often be a fairly direct target of natural or sexual selection, it cannot evolve without changes in subordinate traits that cause or permit its expression. In principle, changes in endocrine function could be a common mechanism underlying behavioral evolution because they are well positioned to mediate integrated responses to behavioral selection. More specifically, hormones can influence both motivational (e.g., brain) and performance (e.g., muscles) components of behavior simultaneously and in a coordinated fashion. If the endocrine system is often "used" as a general mechanism to effect responses to selection, then correlated responses in other aspects of behavior, life history, and organismal performance (e.g., locomotor abilities) should commonly occur because any cell with appropriate receptors could be affected. Ways in which behavior coadapts with other aspects of the phenotype can be studied directly through artificial selection and experimental evolution. Several studies have targeted rodent behavior for selective breeding and reported changes in other aspects of behavior, life history, and lower-level effectors of these organismal traits, including endocrine function. One example involves selection for high levels of voluntary wheel running, one aspect of physical activity, in four replicate High Runner (HR) lines of mice. Circulating levels of several hormones (including insulin, testosterone, thyroxine, triiodothyronine) have been characterized, three of which-corticosterone, leptin, and adiponectin-differ between HR and control lines, depending on sex, age, and generation. Potential changes in circulating levels of other behaviorally and metabolically relevant hormones, as well as in other components of the endocrine system (e.g., receptors), have yet to be examined. Overall, results to date identify promising avenues for further studies on the endocrine basis of activity levels. © The Author 2016. Published by Oxford University

The association between mild geriatric depression and reproductive history--a Darwinian approach.

PubMed

Kirchengast, Sylvia; Haslinger, Beatrix

2010-01-01

The well described trend of population ageing results in a dramatic increase in the number of elderly, reporting symptoms of depression, the most common mood disorder today. Various intrinsic and extrinsic factors are discussed to be responsible for this increase of mood disorders. In the present study the association patterns between mild geriatric depression and the individual reproductive history are analyzed. 264 subjects, 167 females and 97 males, ageing between 60 and 95 years (mean 72.3, SD 8.1 yrs) were enrolled in the present study. The prevalence of depression was tested by mean of the geriatric depression scale (GDS), additionally reproductive history was documented. It turned out, that with increasing number of offspring the depression score decreased. Childless women exhibited the highest prevalence of mild depression and the highest mean depression score. These association patterns between reproductive history and depressive disorders during old age were discussed by means of Darwinian psychiatry. A low number of offspring or childlessness and a lack of social networks for support are new in the evolutionary history of Homo sapiens. Mild geriatric depression may be interpreted as a result of a mismatch or dysregulation because the recent social environment of elderly is completely different from that in which Homo sapiens evolved. The occurrence of geriatric depression may be an adaptation to this new situation.

Co-existence of Distinct Prion Types Enables Conformational Evolution of Human PrPSc by Competitive Selection*

PubMed Central

Haldiman, Tracy; Kim, Chae; Cohen, Yvonne; Chen, Wei; Blevins, Janis; Qing, Liuting; Cohen, Mark L.; Langeveld, Jan; Telling, Glenn C.; Kong, Qingzhong; Safar, Jiri G.

2013-01-01

The unique phenotypic characteristics of mammalian prions are thought to be encoded in the conformation of pathogenic prion proteins (PrPSc). The molecular mechanism responsible for the adaptation, mutation, and evolution of prions observed in cloned cells and upon crossing the species barrier remains unsolved. Using biophysical techniques and conformation-dependent immunoassays in tandem, we isolated two distinct populations of PrPSc particles with different conformational stabilities and aggregate sizes, which frequently co-exist in the most common human prion disease, sporadic Creutzfeldt-Jakob disease. The protein misfolding cyclic amplification replicates each of the PrPSc particle types independently and leads to the competitive selection of those with lower initial conformational stability. In serial propagation with a nonglycosylated mutant PrPC substrate, the dominant PrPSc conformers are subject to further evolution by natural selection of the subpopulation with the highest replication rate due to its lowest stability. Cumulatively, the data show that sporadic Creutzfeldt-Jakob disease PrPSc is not a single conformational entity but a dynamic collection of two distinct populations of particles. This implies the co-existence of different prions, whose adaptation and evolution are governed by the selection of progressively less stable, faster replicating PrPSc conformers. PMID:23974118

Making Heredity Matter: Samuel Butler's Idea of Unconscious Memory.

PubMed

Turbil, Cristiano

2018-03-01

Butler's idea of evolution was developed over the publication of four books, several articles and essays between 1863 and 1890. These publications, although never achieving the success expected by Butler, proposed a psychological elaboration of evolution (robustly enforced by Lamarck's philosophy), called 'unconscious memory'. This was strongly in contrast with the materialistic approach suggested by Darwin's natural selection. Starting with a historical introduction, this paper aspires to ascertain the logic, meaning and significance of Butler's idea of 'unconscious memory' in the post-Darwinian physiological and psychological Pan-European discussion. Particular attention is devoted to demonstrating that Butler was not only a populariser of science but also an active protagonist in the late Victorian psychological debate.

Evolution of Near-Surface Internal and External Oxide Morphology During High-Temperature Selective Oxidation of Steels

NASA Astrophysics Data System (ADS)

Story, Mary E.; Webler, Bryan A.

2018-05-01

In this work we examine some observations made using high-temperature confocal scanning laser microscopy (HT-CSLM) during selective oxidation experiments. A plain carbon steel and advanced high-strength steel (AHSS) were selectively oxidized at high temperature (850-900°C) in either low oxygen or water vapor atmospheres. Surface evolution, including thermal grooving along grain boundaries and oxide growth, was viewed in situ during heating. Experiments investigated the influence of the microstructure and oxidizing atmosphere on selective oxidation behavior. Sequences of CSLM still frames collected during the experiment were processed with ImageJ to obtain histograms that showed a general darkening trend indicative of oxidation over time with all samples. Additional ex situ scanning electron microscopy and energy dispersive spectroscopy analysis supported in situ observations. Distinct oxidation behavior was observed for each case. Segregation, grain orientation, and extent of internal oxidation were all found to strongly influence surface evolution.

Student conceptions of natural selection and its role in evolution

NASA Astrophysics Data System (ADS)

Bishop, Beth A.; Anderson, Charles W.

Pretests and posttests on the topic of evolution by natural selection were administered to students in a college nonmajors' biology course. Analysis of test responses revealed that most students understood evolution as a process in which species respond to environmental conditions by changing gradually over time. Student thinking differed from accepted biological theory in that (a) changes in traits were attributed to a need-driven adaptive process rather than random genetic mutation and sexual recombination, (b) no role was assigned to variation on traits within a population or differences in reproductive success, and (c) traits were seen as gradually changing in all members of a population. Although students had taken an average of 1.9 years of previous biology courses, performance on the pretest was uniformly low. There was no relationship between the amount of previous biology taken and either pretest or posttest performance. Belief in the truthfulness of evolutionary theory was also unrelated to either pretest or posttest performance. Course instruction using specially designed materials was moderately successful in improving students' understanding of the evolutionary process.

The Reciprocal Links between Evolutionary-Ecological Sciences and Environmental Ethics.

ERIC Educational Resources Information Center

Rozzi, Ricardo

1999-01-01

Illustrates the reciprocal relationships between the sciences and environmental ethics by examining the Darwinian theory of evolution and discussing its implications for ecologists and ethicists. (CCM)

Royal Darwinian Demons: Enforced Changes in Reproductive Efforts Do Not Affect the Life Expectancy of Ant Queens.

PubMed

Schrempf, Alexandra; Giehr, Julia; Röhrl, Ramona; Steigleder, Sarah; Heinze, Jürgen

2017-04-01

One of the central tenets of life-history theory is that organisms cannot simultaneously maximize all fitness components. This results in the fundamental trade-off between reproduction and life span known from numerous animals, including humans. Social insects are a well-known exception to this rule: reproductive queens outlive nonreproductive workers. Here, we take a step forward and show that under identical social and environmental conditions the fecundity-longevity trade-off is absent also within the queen caste. A change in reproduction did not alter life expectancy, and even a strong enforced increase in reproductive efforts did not reduce residual life span. Generally, egg-laying rate and life span were positively correlated. Queens of perennial social insects thus seem to maximize at the same time two fitness parameters that are normally negatively correlated. Even though they are not immortal, they best approach a hypothetical "Darwinian demon" in the animal kingdom.

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

Evolution of Cost-Free Resistance under Fluctuating Drug Selection in Pseudomonas aeruginosa

PubMed Central

McCloskey, Nicholas; Hinz, Aaron J.; Dettman, Jeremy; Kassen, Rees

2017-01-01

ABSTRACT Antibiotic resistance evolves rapidly in response to drug selection, but it can also persist at appreciable levels even after the removal of the antibiotic. This suggests that many resistant strains can both be resistant and have high fitness in the absence of antibiotics. To explore the conditions under which high-fitness, resistant strains evolve and the genetic changes responsible, we used a combination of experimental evolution and whole-genome sequencing to track the acquisition of ciprofloxacin resistance in the opportunistic pathogen Pseudomonas aeruginosa under conditions of constant and fluctuating antibiotic delivery patterns. We found that high-fitness, resistant strains evolved readily under fluctuating but not constant antibiotic conditions and that their evolution was underlain by a trade-off between resistance and fitness. Whole-genome sequencing of evolved isolates revealed that resistance was gained through mutations in known resistance genes and that second-site mutations generally compensated for costs associated with resistance in the fluctuating treatment, leading to the evolution of cost-free resistance. Our results suggest that current therapies involving intermittent administration of antibiotics are contributing to the maintenance of antibiotic resistance at high levels in clinical settings. IMPORTANCE Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that

Receiver discriminability drives the evolution of complex sexual signals by sexual selection.

PubMed

Cui, Jianguo; Song, Xiaowei; Zhu, Bicheng; Fang, Guangzhan; Tang, Yezhong; Ryan, Michael J

2016-04-01

A hallmark of sexual selection by mate choice is the evolution of exaggerated traits, such as longer tails in birds and more acoustic components in the calls of birds and frogs. Trait elaboration can be opposed by costs such as increased metabolism and greater predation risk, but cognitive processes of the receiver can also put a brake on trait elaboration. For example, according to Weber's Law traits of a fixed absolute difference will be more difficult to discriminate as the absolute magnitude increases. Here, we show that in the Emei music frog (Babina daunchina) increases in the fundamental frequency between successive notes in the male advertisement call, which increases the spectral complexity of the call, facilitates the female's ability to compare the number of notes between calls. These results suggest that female's discriminability provides the impetus to switch from enhancement of signaling magnitude (i.e., adding more notes into calls) to employing a new signal feature (i.e., increasing frequency among notes) to increase complexity. We suggest that increasing the spectral complexity of notes ameliorates some of the effects of Weber's Law, and highlights how perceptual and cognitive biases of choosers can have important influences on the evolution of courtship signals. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Guiding the evolution to catch the virus: An in silico study of affinity maturation against rapidly mutating antigen

NASA Astrophysics Data System (ADS)

Wang, Shenshen; Burton, Dennis; Kardar, Mehran; Chakraborty, Arup

2014-03-01

The immune system comprises an intricate and evolving collection of cells and molecules that enables a defense against pathogenic agents. Its workings present a rich source of physical problems that impact human health. One intriguing example is the process of affinity maturation (AM) through which an antibody (Ab)--a component of the host immune system--evolves to more efficiently bind an antigen (Ag)--a unique part of a foreign pathogen such as a virus. Sufficiently strong binding to the Ag enables recognition and neutralization. A major challenge is to contain a diversifying mixture of Ag variants, that arise in natural infection, from evading Ab neutralization. This entails a thorough understanding of AM against multiple Ag species and mutating Ag. During AM, Ab-encoding cells undergo cycles of mutation and selection, a process reminiscent of Darwinian evolution yet occurring in real time. We first cast affinity-dependent selection into an extreme value problem and show how the binding characteristics scale with Ag diversity. We then develop an agent-based residue-resolved computational model of AM which allows us to track the evolutionary trajectories of individual cells. This dynamic model not only reveals significant stochastic effects associated with the relatively small and highly dynamic population size, it also uncovers the markedly distinct maturation outcomes if designed Ag variants are presented in different temporal procedures. Insights thus obtained would guide rational design of vaccination protocols.

Lloyd Morgan's theory of instinct: from Darwinism to neo-Darwinism.

PubMed

Richards, R J

1977-01-01

Darwin's proposal of two sources of instinct--natural selection and inherited habit--fostered among late nineteenth century evolutionists a variety of conflicting notions concerning the mechanisms of evolution. The British comparative psychologist C. Lloyd Morgan was a cardinal figure in restructuring the orthodox Darwinian conception to relieve the confusion besetting it and to meet the demands of the new biology of Weismann. This paper traces the development of Morgan's ideas about instinct against the background of his philosophic assumptions and the views of instinct theorists from Darwin and Romanes to McDougall and Lorenz.

On the interplay between mathematics and biology. Hallmarks toward a new systems biology

NASA Astrophysics Data System (ADS)

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M.; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach.

Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

PubMed

Manning, Timmy; Sleator, Roy D; Walsh, Paul

2013-01-01

For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.