Life Sciences Commons^™

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 …

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.

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 …

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 …

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.

Comparative Genomics Of Closely Related Salmonella Enterica Serovar Typhi Strains Reveals Genome Dynamics And The Acquisition Of Novel Pathogenic Elements, Kien-Pong Yap

Kien-Pong Yap

Background Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection.

Results A comparative genomics analysis combined with a phylogenomic analysis revealed that the strains from the outbreak and carrier were closely related with microvariations and possibly derived from a common ancestor. Additionally, the …

Synthesis And Future Directions: What Have Harsh Environments Taught Us About Ecology, Evolution, Conservation, And Restoration?, Nishanta Rajakaruna, Robert S. Boyd, Tanner B. Harris

Nishanta Rajakaruna

No abstract provided.

Phycodnaviruses: A Peek At Genetic Diversity, David Dunigan, Lisa Fitzgerald, James L. Van Etten

David D Dunigan Ph. D.

The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The …

The Geomorphological Evolution Of A Wave-Dominated Barrier Estuary: Burrill Lake, New South Wales, Australia, Brian G. Jones, Craig R. Sloss, David M. Price, C.E. Mcclennen, John De Carli

B. G. Jones

The geomorphological evolution of the Holocene wave-dominated barrier estuary at Burrill Lake on the New South Wales coast, Australia, has been delineated using a combination of seismic stratigraphy and the lithostratigraphic analysis of vibracores collected from the back-barrier estuarine environment. A combination of radiocarbon and aspartic acid racemisation-derived ages obtained on Holocene fossil molluscs, and the thermoluminescent signal in remnant Last Interglacial barrier sediments provides the chronological framework for this investigation. Results from this paper show that the barrier estuary occupies a relatively narrow (<1.5 km wide) and shallow (<40 m deep) incised bedrock valley formed during sea-level …

Cognitive Representation In Transitive Inference: A Comparison Of Four Corvid Species, Alan B. Bond, Cynthia A. Wei, Alan C. Kamil

Alan B. Bond

During operant transitive inference experiments, subjects are trained on adjacent stimulus pairs in an implicit linear hierarchy in which responses to higher ranked stimuli are rewarded. Two contrasting forms of cognitive representation are often used to explain resulting choice behavior. Associative representation is based on memory for the reward history of each stimulus. Relational representation depends on memory for the context in which stimuli have been presented. Natural history characteristics that require accurate configural memory, such as social complexity or reliance on cached food, should tend to promote greater use of relational representation. To test this hypothesis, four corvid species …

Evolution And Sustainability Of The Helping Hands Volunteer Program: Consumer Recovery And Mental Health Comparisoins Six Years On, Frank P. Deane, Retta Andresen

Frank Deane

The Helping Hands program commenced in 1999 and partners volunteers with mental health consumers for support and to increase social contact, recreational and friendship opportunities. The aim of the present study is to describe the evolution and sustainability of the program over the first 6 years. A description of consumers accessing the program using recovery-oriented measures and traditional measures of behavioural functioning is also provided. Service data was collected on the development of the program, service utilisation, volunteer participation and funding patterns. Cross-sectional measures of recovery and baseline and follow-up Health of the Nation Outcome Scales (HoNOS) were collected on …

Celebrating Darwin's Legacy: Evolution In The Galapagos Islands And The Great Plains, Paul A. Johnsgard

Paul Johnsgard

An exhibition of photographs by Linda R. Brown, Josef Kren, Paul A. Johnsgard, Allison Johnson, and Stephen Johnson; paintings by Allison Johnson; drawings by Paul A. Johnsgard; and related Darwiniana. Sponsored by the Center for Great Plains Studies, James Stubbendieck, director, and the Great Plains Art Museum, Amber Mohr, curator, in honor of the bicentennial of Charles Darwin's birth (1809-2009) and the 150th anniversary of The Origin of Species (1859). EXHlBlTORS Linda R. Brown, Lincoln, Nebraska. B.S. (Pharmacy) University of Nebraska-Lincoln, Lincoln, NE, 1965. Paul A. Johnsgard, Lincoln, Nebraska. Foundation Professor Emeritus, University of Nebraska-Lincoln. B.S. (Zoology) North Dakota State …

Quail Music: The Complex Calls Of A Bird Contain Clues To Its Evolution, Paul A. Johnsgard

Paul Johnsgard

Ethological research has revealed that the vocal communications of birds are highly specialized behavioral adaptations that can shed light on evolutionary processes. The calls of the quails of the New World are a good example. This group of birds includes some thirty species, about half of which are limited to the tropical forests of Central and northern South America. The other species are North American, ranging as far north as southern Canada. Morphological evidence favors the view that the most generalized, or “primitive,” of these species are the tree quails of Mexico’s moist mountain forests. The more open-country and arid-adapted …