Digital Commons Network^™

Getting Back To Nature: Feralization In Animals And Plants, Eben Gering, Darren Incorvaia, R. Henriksen, Jeffrey Conner, Thomas Getty, Dominic Wright

Eben Gering

Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how ‘domestication genes’ act in wild settings, studying the brains and …

Tracing Evolutionary Footprints To Identify Novel Gene Functional Linkages., Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Tong He, Fenglou Mao, Congyan Zhang, Huina Zhang, Chaoxing Huo, Pingsheng Liu

Yong Chen

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme …

Robert Koch, Creation, And The Specificity Of Germs, Alan L. Gillen, Douglas Oliver, Frank Sherwin

Alan L. Gillen

Microbiology is dominated by evolution today. Just look at any text, journal article, or the topics presented at professional scientific meetings. Darwin is dominant.

Microbiology is dominated by evolution today. Just look at any text, journal article, or the topics presented at professional scientific meetings. Darwin is dominant. Many argue that “nothing in biology makes sense except in the light of evolution” (Dobzhansky 1973). But it was not always this way. In fact, a review of the major founders of microbiology has shown that they were creationists.1 We would argue that a better idea thanevolution and one of much …

Darwin At The Drugstore? Testing The Biological Fitness Of Antibiotic Resistant Bacteria, Alan L. Gillen, Sarah Anderson

Alan L. Gillen

The issue of antibiotic resistance in bacteria is growing. For example, methicillin-resistant Staphylococcus aureus (MRSA) is a leading human pathogen. New strains of MRSA are resistant to methicillin and numerous other antibiotics, placing the patient in significant danger. Indeed, the Centers for Disease Control revealed in 2007 that the number of deaths due to MRSA exceeded that of AIDS in the United States. It is no wonder that antibiotic resistance is one of the most significant and important health care issues. The ability of bacterial pathogens to evade traditional antibiotics is faster than the drug makers’ ability to make new …

Encoding Of Emotional Valence In Wild Boar (Sus Scrofa) Calls, Anne-Laure Maigrot, Edna Hillmann, Elodie Briefer

Elodie Briefer, PhD

Measuring emotions in nonhuman mammals is challenging. As animals are not able to verbally report how they feel, we need to find reliable indicators to assess their emotional state. Emotions can be described using two key dimensions: valence (negative or positive) and arousal (bodily activation or excitation). In this study, we investigated vocal expression of emotional valence in wild boars (Sus scrofa). The animals were observed in three naturally occurring situations: anticipation of a food reward (positive), affiliative interactions (positive), and agonistic interactions (negative). Body movement was used as an indicator of emotional arousal to control for the effect of …

Proprioception, Non-Law, And Biolegal History, Owen D. Jones

Owen Jones

This Article explores several advantages of incorporating into law various insights from behavioral biology about how and why the brain works as it does. In particular, the Article explores the ways in which those insights can help illuminate the deep structure of human legal systems. That effort is termed "biolegal history."

On The Nature Of Norms: Biology, Morality, And The Disruption Of Order, Owen D. Jones

Owen Jones

This essay discusses the legal implications of bio-behavioral underpinnings to norms, morality, and economic order. It first discusses the recent book "The Great Disruption: Human Nature and the Reconstitution of Social Order," in which Francis Fukuyama explores the importance of evolved human nature to the reconstruction of social order and a thriving economy. It then addresses the extent to which we can usefully view law-relevant norms as products of evolutionary - as well as economic - processes.

Law And Behavioral Biology, Owen D. Jones, Timothy H. Goldsmith

Owen Jones

Society uses law to encourage people to behave differently than they would behave in the absence of law. This fundamental purpose makes law highly dependent on sound understandings of the multiple causes of human behavior. The better those understandings, the better law can achieve social goals with legal tools. In this Article, Professors Jones and Goldsmith argue that many long held understandings about where behavior comes from are rapidly obsolescing as a consequence of developments in the various fields constituting behavioral biology. By helping to refine law's understandings of behavior's causes, they argue, behavioral biology can help to improve law's …

Evolutionary Analysis In Law: Some Objections Considered, Owen D. Jones

Owen Jones

This Article appears in a special issue of the Brooklyn Law Review on DNA: Lessons from the Past - Problems for the Future. It first addresses why law needs insights from behavioral biology, and then identifies and responds to a variety of structural and conceptual barriers to such evolutionary analysis in law.

A Novel Body Coloration Phenotype In Anolis Sagrei: Implications For Physiology, Fitness, And Predation, Yasmeen Erritouni, Beth Reinke, Ryan Calsbeek

Beth Reinke

The Positive Effect Of Role Models In Evolution Instruction, Emily A. Holt, T. Heath Ogden, Susan L. Durham

T. Heath Ogden

Characterizing The Evolutionary Path(S) To Early Homo, Lauren Schroeder, Charles C. Roseman, James M. Cheverud, Rebecca R. Ackermann

James Cheverud

Numerous studies suggest that the transition from Australopithecus to Homo was characterized by evolutionary innovation, resulting in the emergence and coexistence of a diversity of forms. However, the evolutionary processes necessary to drive such a transition have not been examined. Here, we apply statistical tests developed from quantitative evolutionary theory to assess whether morphological differences among late australopith and early Homo species in Africa have been shaped by natural selection. Where selection is demonstrated, we identify aspects of morphology that were most likely under selective pressure, and determine the nature (type, rate) of that selection. Results demonstrate that selection must …

Diaspora, A Large Family Of Ty3-Gypsy Retrotransposons In Glycine Max, Is An Envelope-Less Member Of An Endogenous Plant Retrovirus Lineage, Sho T. Yano, Bahman Panbehi, Arpita Das, Howard M. Laten

Howard Laten

Background The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful colonizers of the chromosomes of higher plants and examinations of their function, evolution, and dispersal are essential to understanding the evolution of eukaryotic genomes. In soybean, several families of retrotransposons have been identified, including at least two that, by virtue of the presence of an envelope-like gene, may constitute endogenous retroviruses. However, most elements are highly degenerate and are often sequestered in regions of the genome that sequencing projects initially …

Adaptive Evolution And Inherent Tolerance To Extreme Thermal Environments, Jennifer Cox, Alyxandria Schubert, Michael Travisano, Catherine Putonti

Catherine Putonti

Background When introduced to novel environments, the ability for a species to survive and rapidly proliferate corresponds with its adaptive potential. Of the many factors that can yield an environment inhospitable to foreign species, phenotypic response to variation in the thermal climate has been observed within a wide variety of species. Experimental evolution studies using bacteriophage model systems have been able to elucidate mutations, which may correspond with the ability of phage to survive modest increases/decreases in the temperature of their environment. Results Phage ΦX174 was subjected to both elevated (50°C) and extreme (70°C+) temperatures for anywhere from a few …

A Review Of The Institute Of Medicine’S Analysis Of Using Chimpanzees In Biomedical Research, Robert C. Jones, Ray Greek

Robert C. Jones, PhD

We argue that the recommendations made by the Institute of Medicine’s 2011 report, Chimpanzees in Biomedical and Behavioral Research: Assessing the Necessity, are methodologically and ethically confused. We argue that a proper understanding of evolution and complexity theory in terms of the science and ethics of using chimpanzees in biomedical research would have had led the committee to recommend not merely limiting but eliminating the use of chimpanzees in biomedical research. Specifically, we argue that a proper understanding of the difference between the gross level of examination of species and examinations on finer levels can shed light on important methodological …

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel I. Speiser, M. Sabrina Pankey, Alexander K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Anja S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Meredith Protas

Background: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to …

Opsin Repertoire And Expression Patterns In Horseshoe Crabs: Evidence From The Genome Of Limulus Polyphemus (Arthropoda: Chelicerata), Barbara-Anne Battelle, Joseph F. Ryan, Karen E. Kempler, Spencer R. Saraf, Catherine E. Marten, Wesley C. Warren, Patrick J. Minx, Michael J. Montague, Pamela J. Green, Skye A. Schmidt, Lucinda Fulton, Nipam H. Patel, Meredith E. Protas, Richard K. Wilson, Megan L. Porter

Meredith Protas

Horseshoe crabs are xiphosuran chelicerates, the sister groupto arachnids. As such, they are important for understandingthemost recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and …

Fish Pain: An Inconvenient Truth, Culum Brown

Culum Brown, PhD

Whether fish feel pain is a hot political topic. The consequences of our denial are huge given the billions of fish that are slaughtered annually for human consumption. The economic costs of changing our commercial fishery harvest practices are also likely to be great. Key outlines a structure-function analogy of pain in humans, tries to force that template on the rest of the vertebrate kingdom, and fails. His target article has so far elicited 34 commentaries from scientific experts from a broad range of disciplines; only three of these support his position. The broad consensus from the scientific community is …

The Incredible Shrinking Dewlap: Signal Size, Skin Elasticity, And Mechanical Design In The Green Anole Lizard (Anolis Carolinensis), Simon Lailvaux, Jack Leifer, Bonnie Kircher, Michele Johnson

Jack Leifer

The expression of male secondary sexual traits can be dynamic, changing size, shape, color, or structure over the course of different seasons. However, the factors underlying such changes are poorly understood. In male Anolis carolinensis lizards, a morphological secondary sexual signal called the dewlap changes size seasonally within individuals. Here, we test the hypothesis that seasonal changes in male dewlap size are driven by increased use and extension of the dewlap in spring and summer, when males are breeding, relative to the winter and fall. We captured male green anole lizards prior to the onset of breeding and constrained the …

Is Your Learning Style Paranoid?, Kirby Farrell

kirby farrell

We learn—and grow—by engaging with anomalies: new things that don't fit our familiar categories. It's a gut process, not just a philosophical choice. Anxiety can make us paranoid about what's new and strange. Knowing that can spur fascination and help us to adapt.

Biomaterial Evolution Parallels Behavioral Innovation In The Origin Of Orb-Like Spider Webs, Todd Blackledge, Matjaz Kuntner, Mohammad Marhabaie, Thomas Leeper

Thomas C Leeper

Correlated evolution of traits can act synergistically to facilitate organism function. But, what happens when constraints exist on the evolvability of some traits, but not others? The orb web was a key innovation in the origin of >12,000 species of spiders. Orb evolution hinged upon the origin of novel spinning behaviors and innovations in silk material properties. In particular, a new major ampullate spidroin protein (MaSp2) increased silk extensibility and toughness, playing a critical role in how orb webs stop flying insects. Here, we show convergence between pseudo-orb-weaving Fecenia and true orb spiders. As in the origin of true orbs, …

The Evolutionary History Of Cetacean Brain And Body Size, Stephen H. Montgomery, Jonathan H. Geisler, Michael R. Mcgowen, Charlotte Fox, Lori Marino, John Gatesy

Lori Marino, PhD

Cetaceans rival primates in brain size relative to body size and include species with the largest brains and biggest bodies to have ever evolved. Cetaceans are remarkably diverse, varying in both phenotypes by several orders of magnitude, with notable differences between the two extant suborders, Mysticeti and Odontoceti.We analyzed the evolutionary history of brain and body mass, and relative brain size measured by the encephalization quotient (EQ), using a data set of extinct and extant taxa to capture temporal variation in the mode and direction of evolution. Our results suggest that cetacean brain and body mass evolved under strong directional …

Life History Evolution And Adaptive Radiation Of Hemidactyliine Salamanders, Travis Ryan, R. Bruce

Travis J. Ryan

T.J. Ryan and R.C. Bruce's contribution to: The Biology of Plethodontid Salamanders, R. C. Bruce, R. G. Jaeger, and L. D. Houck, eds. Kluwer Academic/Plenum Publishers, New York.

Development Of An Interactive Course Module: "Teaching And Learning Molecular Basis Of Evolution To Human Body", Soma Mukhopadhyay, Rachel Bishop, Brittany Blocker

Soma Mukhopadhyay Ph.D.

Today’s youth expect to use technology in every aspect of their lives, including their education. Instead of being challenged by their considerable skills, educators should embrace the technology and use it to make the classroom experience more enjoyable for students, thereby improving learning outcomes. Evolution is no different – students must know the basics of evolution in order to be well-read members of society, and technology can help the students learn. The study of evolution today is incredibly interesting, particularly with new evidence coming to light almost daily. Human evolution, in particular, is the subject of copious amounts of research. …

High-Performance Spider Webs: Integrating Biomechanics, Ecology And Behaviour, Todd Blackledge, Aaron Harmer, Joshua Madin, Marie Herberstein

Todd A. Blackledge

Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence …

Biomaterial Evolution Parallels Behavioral Innovation In The Origin Of Orb-Like Spider Webs, Todd Blackledge, Matjaz Kuntner, Mohammad Marhabaie, Thomas Leeper

Todd A. Blackledge

Correlated evolution of traits can act synergistically to facilitate organism function. But, what happens when constraints exist on the evolvability of some traits, but not others? The orb web was a key innovation in the origin of >12,000 species of spiders. Orb evolution hinged upon the origin of novel spinning behaviors and innovations in silk material properties. In particular, a new major ampullate spidroin protein (MaSp2) increased silk extensibility and toughness, playing a critical role in how orb webs stop flying insects. Here, we show convergence between pseudo-orb-weaving Fecenia and true orb spiders. As in the origin of true orbs, …

The Phylogenetic Placement Of Psechridae Within Entelegynae And The Convergent Origin Of Orb-Like Webs, Todd Blackledge, Matjaz Gregoric, Matjaz Kuntner, Ingi Agnarsson

Todd A. Blackledge

Evolutionary convergence of phenotypic traits provides evidence for their functional success. The origin of the orb web was a critical event in the diversification of spiders that facilitated a spectacular radiation of approximately 12 000 species and promoted the evolution of novel web types. How the orb web evolved from ancestral web types, and how many times orb-like architectures evolved in spiders, has been debated for a long time. The little known spider genus Fecenia (Psechridae) constructs a web that resembles the archetypical orb web, but morphological data suggest that Psechridae (Psechrus + Fecenia) does not belong in Orbiculariae, the …

Herbert W. Conn: Formative Decades Of Microbiology And Evolutionary Biology, Frederick M. Cohan, Alexa Boesel

Frederick M. Cohan

Herbert W. Conn (1859–1917) made outstanding contributions to both microbiology and evolutionary biology, reflecting his intellectual command of several biological disciplines. Conn endeavored to make the unseen world of microbes familiar, real, and consequential to members of the general public. He presciently considered the role of bacteria in our own bodies, describing them as being both harmful and beneficial to our health. He also contributed to our understanding of the concept of species, how they originate, and what those ideas might mean in terms of bacterial speciation. In Conn’s spirit, microbial ecologists studying speciation eschew the “species” taxa of bacterial …

Phylogeny Of Family Limnephilidae (Insecta: Trichoptera) With Emphasis On Tribe Limnephilini (Subfamily Limnephilinae), Tatyana Vshivkova

John C Morse

Morphological characters of adults and immature stages of Limnephilidae were analyzed with modern phylogenetic techniques, including traditionally used characters and some that have been poorly investigated or never studied. For the first time, monophyly is inferred for the following nominotypical taxa: superfamily Limnephiloidea, family Limnephilidae, subfamily Limnephilinae, tribe Limnephilini, and Limnephilus sensu stricto. Some other higher taxa are distinguished based on high bootstrap support, unreversed synapomorphies, and/or topography, including a new family-group category for Trichoptera, 'Branch,' more inclusive than the family category and less inclusive than the superfamily category. These new taxa in Limnephiloidea are as follows: Brachycentrida New Branch …

The Failure Of Evolution In Antiquity, Devin Henry

Devin Henry

This paper traces the emergence and rejection of evolutionary thinking in antiquity. It examines Empedocles' original theory of evolution and why his ideas failed to gain traction among his predecessors.