Life Sciences Commons^™

Drug-Resistant Hiv-1 Protease Regains Functional Dynamics Through Cleavage Site Coevolution, Nevra Ozer, Aysegul Ozen, Celia Schiffer, Turkan Haliloglu

Celia A. Schiffer

Drug resistance is caused by mutations that change the balance of recognition favoring substrate cleavage over inhibitor binding. Here, a structural dynamics perspective of the regained wild-type functioning in mutant HIV-1 proteases with coevolution of the natural substrates is provided. The collective dynamics of mutant structures of the protease bound to p1-p6 and NC-p1 substrates are assessed using the Anisotropic Network Model (ANM). The drug-induced protease mutations perturb the mechanistically crucial hinge axes that involve key sites for substrate binding and dimerization and mainly coordinate the intrinsic dynamics. Yet with substrate coevolution, while the wild-type dynamic behavior is restored in …

Growth And The Expression Of Alternative Life Cycles In The Salamander Ambystoma Talpoideum (Caudata: Ambystomatidae), Travis Ryan, Raymond Semlitsch

Travis J. Ryan

Complex life cycles (CLCs) contain larval and adult phases that are morphologically and ecologically distinct. Simple life cycles (SLCs) have evolved from CLCs repeatedly in a wide variety of lineages but the processes that may underlie the transition have rarely been identified or investigated experimentally. We examined the influence of larval growth rate on the facultative expression of alternative life cycles (metamorphosis or maturation as gill-bearing adults [= paedomorphosis]) in the salamander Ambystoma talpoideum. We manipulated growth rates by altering the amount of food individuals received throughout larval development. The expression of alternative life cycles in A. talpoideum is influenced …

The Orientation Of Strophomenid Brachiopods On Soft Substrates, Roy Plotnick, Benjamin Dattilo, Daniel Piquard, Jennifer Bauer, Joshua Corrie

Benjamin F. Dattilo

Strophomenid brachiopods have long been interpreted as ‘‘snowshoe’’ strategists, with their flattened concavoconvex valves providing resistance to foundering in very soft sediments. There has been a sharp difference of opinion in whether the shells were oriented with their convex or their concave surface in contact with the sediment. This study, along with independent evidence from sedimentology, ichnology, and morphology, indicates that the strophomenids lived with their shells concave down (convex up). Experiments indicate the force required to push shells into soft cohesive muds is much greater for the convex up than for the convex down orientation. Forces also increase with …

The First Molecular Phylogeny Of Buthidae (Scorpiones), Victor Fet, Benjamin Gantenbein, Alexander Gromov, Graeme Lowe, Wilson Lourenço

Victor Fet

The first partial phylogeny of family Buthidae (17 genera) is presented, based on molecular data (16S rRNA mitochondrial DNA). The strong support for a monophyletic Old World group of 13 genera (mainly Palearctic desert forms) is demonstrated, while representative genera from Madagascar (Grosphus) and Southeast Asia (Lychas) group outside, as well as New World genera Centruroides and Rhopalurus. A very strong support is observed for the first time for three groups of Old World genera: (a) Compsobuthus, Mesobuthus, Liobuthus, Kraepelinia; (b) Hottentotta, Buthacus; (c) Orthochirus, Anomalobuthus. Phylogenetic hypotheses are discussed.

Etudes On Iurids, V. Further Revision Of Iurus Thorell, 1876 (Scorpiones: Iuridae), With A Description Of A New Genus And Two New Species, Michael Soleglad, Victor Fet, František Kovařík, Ersen Yağmur

Victor Fet

Iurus populations from the Aegean area are studied, including the Greek islands of Crete, Karpathos, Kythira, Rhodes, and Samos. A new genus, Protoiurus gen. nov., and two new species, Protoiurus rhodiensis sp. nov. and P. stathiae sp. nov., are described. The two genera, Iurus and Protoiurus, are diagnosed by their hemispermatophore structure; a cladistic analysis based on this structure is presented. Genus Iurus Thorell, 1876 includes three species: I. dekanum, I. dufoureius, and I. kinzelbachi; genus Protoiurus includes five species: P. asiaticus comb. nov., P. kadleci comb. nov., P. kraepelini comb. nov., P. rhodiensis sp. nov., and P. stathiae sp. …

The Cretaceous Scorpion Genus, Archaeobuthus, Revisited (Scorpiones: Archaeobuthidae), Chris Baptista, Jorge Santiago-Blay, Victor Fet, Michael Soleglad

Victor Fet

No abstract provided.

Molecular Pedomorphism Underlies Craniofacial Skeletal Evolution In Antarctic Notothenioid Fishes, R. Albertson, Yi-Lin Yan, Tom Titus, Eva Pisano, Marino Vacchi, Pamela Yelick, H. Detrich, John Postlethwait

H. William Detrich III

Background Pedomorphism is the retention of ancestrally juvenile traits by adults in a descendant taxon. Despite its importance for evolutionary change, there are few examples of a molecular basis for this phenomenon. Notothenioids represent one of the best described species flocks among marine fishes, but their diversity is currently threatened by the rapidly changing Antarctic climate. Notothenioid evolutionary history is characterized by parallel radiations from a benthic ancestor to pelagic predators, which was accompanied by the appearance of several pedomorphic traits, including the reduction of skeletal mineralization that resulted in increased buoyancy. Results We compared craniofacial skeletal development in two …

Compilation, Calibration, And Synthesis Of Faunal And Floral Radiocarbon Dates, Rancho La Brea, California, F. O’Keefe, Elizabeth Fet, John Harris

F. Robin O’Keefe

This paper presents a compilation and synthesis of calibrated radiocarbon dates for the Rancho La Brea tar pits, Los Angeles, California. A literature survey yielded 188 dates, and 21 additional dates are presented here for the first time. These range in age from 185 to 50,000 radiocarbon years. Dating of Rancho La Brea fossils has been uneven; only from Pits 91 and 2051 have more than 30 dates been obtained. The depositional history of well-sampled pits was complex, with one or more episodes of major accumulation interspersed with lower background levels of entrapment. The most significant quantifiable source of error …

Extreme Environments Select For Reproductive Assurance: Evidence From Evening Primroses (Oenothera), Margaret Evans, David Hearn, Kathryn Theiss, Karen Cranston, Kent Holsinger, Michael Donoghue

Kent E Holsinger

• Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, eco- logical conditions, and geographical context. Here, we examined two such predictions: that self-compatibility should be associated with the annual life history or extreme climatic conditions.

• We analyzed data from a clade of plants remarkable for variation in breeding system, life history and climatic conditions (Oenothera, sections Anogra and Kleinia, Onagraceae). We used a phylogenetic comparative approach and Bayesian or hybrid Bayesian tests to account …

The Behavioural And Sensory Ecology Of Agaronia Propatula (Caenogastropoda, Olividae), A Swash-Surfing Predator On Sandy Beaches Of The Panamic Faunal Province, Ariel Cyrus, Samantha Rupert, Amy Silva, Monika Graf, Jeremy Rappaport, Frank Paladino, Winfried Peters

Winfried S. Peters

On Characterizing Adaptive Events Unique To Modern Humans, Jessica Crisci, Alex Wong, Jeffrey Good, Jeffrey Jensen

Jessica L Crisci

Ever since the first draft of the human genome was completed in 2001 there has been increased interest in identifying genetic changes that are uniquely human, which could account for our distinct morphological and cognitive capabilities with respect to other apes. Recently, draft sequences of two extinct hominin genomes, a Neanderthal and Denisovan, have been released. These two genomes provide a much greater resolution to identify human-specific genetic differences than the chimpanzee, our closest extant relative. The Neanderthal genome paper presented a list of regions putatively targeted by positive selection around the time of the human-Neanderthal split. We here seek …

Recent Progress In Polymorphism-Based Population Genetic Inference., Jessica Crisci, Yu-Ping Poh, Angela Bean, Alfred Simkin, Jeffrey Jensen

Jessica L Crisci

The recent availability of whole-genome sequencing data affords tremendous power for statistical inference. With this, there has been great interest in the development of polymorphism-based approaches for the estimation of population genetic parameters. These approaches seek to estimate, for example, recently fixed or sweeping beneficial mutations, the rate of recurrent positive selection, the distribution of selection coefficients, and the demographic history of the population. Yet despite estimating similar parameters using similar data sets, results between methodologies are far from consistent. We here summarize the current state of the field, compare existing approaches, and attempt to reconcile emerging discrepancies. We also …

Do Larval Traits Re-Evolve? Evidence From The Embryogenesis Of A Direct-Developing Salamander, Plethodon Cinereus, Ryan Kerney, David Blackburn, Hendrik Muller, James Hanken

Ryan Kerney

Recent molecular phylogenies suggest the surprising reacquisition of posthatching metamorphosis within an otherwise directdeveloping clade of lungless salamanders (family Plethodontidae). Metamorphosis was long regarded as plesiomorphic for plethodontids, yet the genus Desmognathus, which primarily includes metamorphosing species, is now nested within a much larger clade of direct-developing species. The extent to which the putative reacquisition of metamorphosis in Desmognathus represents a true evolutionary reversal is contingent upon the extent to which both larva-specific features and metamorphosis were actually lost during the evolution of direct development. In this study we analyze development of the hyobranchial skeleton, which is dramatically remodeled during …

Intracellular Invasion Of Green Algae In A Salamander Host, Ryan Kerney, Eunsoo Kim, Roger Hangater, Aaron Heiss, Cory Bishop, Brian Hall

Ryan Kerney

The association between embryos of the spotted salamander (Ambystoma maculatum) and green algae (“Oophila amblystomatis” Lamber ex Printz) has been considered an ectosymbiotic mutualism. We show here, however, that this symbiosis is more intimate than previously reported. A combination of imaging and algal 18S rDNA amplification reveals algal invasion of embryonic salamander tissues and cells during development. Algal cells are detectable from embryonic and larval Stages 26–44 through chlorophyll autofluorescence and algal 18S rDNA amplification. Algal cell ultrastructure indicates both degradation and putative encystment during the process of tissue and cellular invasion. Fewer algal cells were detected in later-stage larvae …

Symbioses Between Salamander Embryos And Green Algae, Ryan Kerney

Ryan Kerney

The symbiosis between Ambystoma maculatum (spotted salamander) embryos and green algae was initially described over 120 years ago. Algae populate the egg capsules that surround individual A. maculatum embryos, giving the intracapsular fluid a characteristic green hue. Early work established this symbiosis to be a mutualism, while subsequent studies sought to identify the material benefits of this association to both symbiont and host. These studies have shown that salamander embryos benefit from increased oxygen concentrations provided by their symbiotic algae. The algae, in turn, may benefit from ammonia excreted by the embryos. All of these early studies considered the associ- …

Plant-Animal Interactions, W. Abrahamson, T. Taylor

Warren G. Abrahamson, II

No abstract provided.

Access To Mutualistic Endosymbiotic Microbes: An Underappreciated Benefit Of Group Living, Michael Lombardo

Michael P Lombardo

"The original publication is available at www.springerlink.com"

A central question in behavioral ecology has been why animals live in groups. Previous theories about the evolution of sociality focused on the potential benefits of decreased risk of predation, increased foraging or feeding efficiency, and mutual aid in defending resources and/or rearing offspring. This paper argues that access to mutualistic endosymbiotic microbes is an underappreciated benefit of group living and sets out to reinvigorate Troyer’s hypothesis that the need to obtain cellulolytic microbes from conspecifics influenced the evolution of social behavior in herbivores and to extend it to nonherbivores. This extension is …

On The Evolution Of Sexually Transmitted Diseases In Birds, Michael Lombardo

Michael P Lombardo

"The definitive version is available at www.blackwell-synergy.com".

Sexually transmitted diseases (STDs) in animals are caused by pathogens that are transmitted during copulation. Birds have played an important role in the development of STD-centered theories of mating behavior. However, it is not known whether STDs exist in wild bird populations. While the avian cloaca with its dual functions of gamete transfer and excretion seemingly predisposes birds for the evolution of STDs, the life history patterns of most birds (i.e., seasonal breeders with relatively brief annual periods of sexual activity) suggest otherwise. The importance of STDs as selective forces that shape host …

Early Cranial Patterning In The Direct-Developing Frog Eleutherodactylus Coqui Revealed Through Gene Expression, Ryan Kerney, Joshua Gross, James Hanken

Ryan Kerney

Genetic and developmental alterations associated with the evolution of amphibian direct development remain largely unexplored. Specifically, little is known of the underlying expression of skeletal regulatory genes, which may reveal early modifications to cranial ontogeny in direct-developing species. We describe expression patterns of three key skeletal regulators (runx2, sox9, and bmp4) along with the cartilage-dominant collagen 2a1 gene (col2a1) during cranial development in the direct- developing anuran, Eleutherodactylus coqui. Expression patterns of these regulators reveal transient skeletogenic anlagen that correspond to larval cartilages, but which never fully form in E. coqui. Suprarostral anlagen in the frontonasal processes are detected through …

Darwinian Controversies: An Historiographical Recounting, David Depew

David J Depew

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 …

Gene Expression Reveals Unique Skeletal Patterning In The Limb Of The Direct-Developing Frog, Eleutherodactylus Coqui, Ryan Kerney, James Hanken

Ryan Kerney

The growing field of skeletal developmental biology provides new molecular markers for the cellular pre- cursors of cartilage and bone. These markers enable resolution of early features of skeletal development that are otherwise undetectable through conventional staining tech- niques. This study investigates mRNA distributions of skeletal regulators runx2 and sox9 along with the cartilage-dominant collagen 2a1 (col2a1) in embryonic limbs of the direct- developing anuran, Eleutherodactylus coqui. To date, distri- butions of these genes in the limb have only been examined in studies of the two primary amniote models, mouse and chicken. In E. coqui, expression of transcription factors runx2 …

Inheriting Inherit The Wind: Debating The Play As A Teaching Tool, Edward Larson, David Depew, Ronald Isetti

David J Depew

No abstract provided.

Hydroperiod And Metamorphosis In The Small-Mouthed Salamander

Travis J. Ryan

Runx2 Is Essential For Larval Hyobranchial Cartilage Formation In Xenopus Laevis, Ryan Kerney, Joshua Gross, James Hanken

Ryan Kerney

The vertebrate transcription factor protein Runx2 is regarded as a “master regulator” of bone formation due to the dramatic loss of the osseous skeleton in the mouse homozygous knockout. However, Runx2 mRNA also is expressed in the pre-hypertrophic cartilaginous skeleton of the mouse and chicken, where its developmental function is largely unknown. Several tiers of Runx2 regulation exist in the mouse, any of which may account for its seeming biological inactivity during early stages of skeletogenesis. Unlike mouse and chicken, zebrafish require Runx2 function in early cartilage differentiation. The present study reveals that the earlier functional role of Runx2 in …

Legacy Of Land Use In Southern Appalachian Forests: Effects On Terrestrial Salamander Abundance Along Edges And Within Abandoned Logging Roads, R. Semlitsch,, Travis Ryan, M. Chatfield, B. Drehman, K. Hamed, N. Pekarek, M. Spath

Travis J. Ryan

Presence And Colonization Of Placobdella On Two Species Of Freshwater Turtles (Graptemys Geographica And Sternotherus Odoratus), Travis Ryan

Travis J. Ryan

It is generally accepted that bottom-dwelling turtles have a higher ectoparasite load than turtles that bask aerially because of effects of desiccation on ectoparasites, especially with regard to leeches. We compared number of leeches (primarily Placobdella parasitica) on field-caught Common Musk Turtles (Stemotherus odoratus) and Common Map Turtles (Graptemys geographica). The bottom-dwelling species S. odoratus had more than 20 times the number of leeches than the aerial-basking species G. geographica. We then exposed cleaned (leech-free) turtles to leeches in mesocosms (cattle tanks) to measure the rate of colonization. In this experiment, S. odoratus had more than four times the number …

Darwinism, Design And Complex Systems Dynamics, David Depew, Bruce Weber

David J Depew

No abstract provided.

Evolution And Learning: The Baldwin Effect Reconsidered, David Depew, Bruce Weber

David J Depew

The role of genetic inheritance dominates current evolutionary theory. At the end of the nineteenth century, however, several evolutionary theorists independently speculated that learned behaviors could also affect the direction and rate of evolutionary change. This notion was called the Baldwin effect, after the psychologist James Mark Baldwin. In recent years, philosophers and theorists of a variety of ontological and epistemological backgrounds have begun to employ the Baldwin effect in their accounts of the evolutionary emergence of mind and of how mind, through behavior, might affect evolution.

The essays in this book discuss the originally proposed Baldwin effect, how it …

Developmental Systems, Darwinian Evolution,And The Unity Of Science, Bruce Weber, David Depew

David J Depew

No abstract provided.

Genetic Biotechnology And Evolutionary Theory: Some Unsolicited Advice, David Depew

David J Depew

In his book The Biotech Century Jeremy Rifkin makes arguments about the dangers of market-driven genetic biotechnology in medical and agricultural contexts. Believing that Darwinism is too compromised by a competitive ethic to resist capitalist depredations of the “genetic commons,” and perhaps hoping to pick up anti-Darwinian allies, he turns for support to unorthodox non-Darwinian views of evolution. The Darwinian tradition, more closely examined, contains resources that might better serve his argument. The robust tradition associated with Theodosius Dobzhansky, Ernst Mayr, and others provides an alternative, scientifically sound basis for challenging the rhetoric of genetic reductionism.