Distinguishing ecological from evolutionary approaches to transposable elements

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology

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Whispering to the Deaf: Communication by a Frog without External Vocal Sac or Tympanum in Noisy Environments

Atelopus franciscus is a diurnal bufonid frog that lives in South-American tropical rain forests. As in many other frogs, males produce calls to defend their territories and attract females. However, this species is a so-called “earless” frog lacking an external tympanum and is thus anatomically deaf. Moreover, A. franciscus has no external vocal sac and lives in a sound constraining environment along river banks where it competes with other calling frogs. Despite these constraints, male A. franciscus reply acoustically to the calls of conspecifics in the field. To resolve this apparent paradox, we studied the vocal apparatus and middle-ear, analysed signal content of the calls, examined sound and signal content propagation in its natural habitat, and performed playback experiments. We show that A. franciscus males can produce only low intensity calls that propagate a short distance (<8 m) as a result of the lack of an external vocal sac. The species-specific coding of the signal is based on the pulse duration, providing a simple coding that is efficient as it allows discrimination from calls of sympatric frogs. Moreover, the signal is redundant and consequently adapted to noisy environments. As such a coding system can be efficient only at short-range, territory holders established themselves at short distances from each other. Finally, we show that the middle-ear of A. franciscus does not present any particular adaptations to compensate for the lack of an external tympanum, suggesting the existence of extra-tympanic pathways for sound propagation

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Conceptual and empirical challenges of ascribing functions to transposable elements

The media attention and subsequent scientific backlash engendered by the claim, announced by spokespeople for the Encyclopedia of DNA Elements project (ENCODE), that 80% of the human genome has a “biochemical function” highlights the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science – the “causal role” concept and the “selected effects” concept – and their relevance to ENCODE. Unlike some previous critiques, the ENCODE project is not considered problematic because it employed a causal role definition of function (which is relatively common in genetics), but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements (TEs), but which were ignored by ENCODE, are highlighted. These include issues surrounding TE-level versus organism-level selection, the origins versus the persistence of elements, and accidental versus functional organism-level benefits. Finally, some key questions are presented that should be addressed in any studies aiming to ascribe functions to major portions of large eukaryotic genomes, the majority of which is made up of transposable elements

Low Cost Metal Chip Separator

We were tasked by Micro-Vu to design, build, and test a small-scale low-cost metal chip separator to operate on one of their 24/7 mills. The goal of the project was to separate the steel and aluminum chips coming off of the mill’s chip conveyor to end up with a bin of 99% pure aluminum by mass. To accomplish this goal we first brainstormed various possible ideas and performed small scale tests the best ones. After further review we determined the best solution to this problem was a design that involved a cycling magnetic backing that would pull steel out of the flow and drop it into a separate bin. To prove our concept we build a small scale wooden mockup. After running various tests using this mockup we determined that our design was a viable solution to the problem. We then moved on to completing our final design and building the prototype. In the end the prototype was fully functional and in testing was able to separate metal chips and achieve a separation rate of 92-99% separation by mass

Failure Analysis of Investment Cast Near-Alpha Titanium Alloys

In this project, fracture surfaces of three titanium investment castings were studied as part of a failure analysis on a TaylorMade metalwood. The crack formation occurred between investment cast Ti 9-1-1 and rolled Ti 6-4 joined by laser beam welding. The microstructure of the Ti 9-1-1 contained alpha colonies in large prior beta grains, while the Ti 6-4 was primarily Widmanstätten in basket weave morphology, refined with subsequent rolling. Over a period of cyclic loading, cracking occurred at the face-sole transition in the metalwoods that had been cast from a certain supplier B, while metalwoods that had undergone similar treatment from another supplier, did not exhibit any cracks. In order to understand the reason for this discrepancy, the fracture surfaces of the cracked metalwoods were examined and imaged with a scanning electron microscope (SEM) in order to study the mode and method of failure. The fracture surfaces examined occurred at a geometric transition, where internal stresses were higher according to FEA. Furthermore, the fracture surfaces revealed lack of fusion in no-fill regions occurring at this transition, where microcracks were observed to be initiating. These pores were most likely the source of fatigue crack initiation, if not, accelerating the propagation of the crack to final rupture

Applying ecological models to communities of genetic elements: the case of neutral theory

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size