Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size - 0.6pg to 4.4 pg per haploid cell. Firstly, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree - the first between 43-49 Mya (95% highest posterior density (HPD) 36.2-68.1 Mya) and the second at ~19 Mya (95% HPD 15.3-30.14 Mya). Secondly, RAD sequencing was used to identify potential WGD events and quantify transposable element abundance in different lineages. Evidence of two lineage scale WGDs were identified across the phylogeny, the first event occurring between 54-66 Mya (95% HPD 42.56-99.5 Mya) and the second at 20-30 Mya (95% HPD 15.3-45 Mya) based on haplotype numbers per contig and between 35-44 Mya (95% HPD 30.29-64.51 Mya) and 20-30 Mya (95% HPD 15.3-45 Mya) based on SNP read ratios. Transposable element abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20-30 Mya (95% HPD 15.3-45 Mya) and an older event at 35-44 Mya (95% HPD 30.29-64.51 Mya). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution

Away with the Apprentice: Graduate Worker Advocacy Groups and Rhetorical Representation

While graduate workers have a long history of organizing and advocating on their own behalf, concerns specific to their unique identity as both laborers and students have not yet permeated the discourse surrounding worker rights in higher education. Using Edward Schiappa’s work on how definitions are created and circulated, I position that the work and labor of the graduate student is under-discoursed because of the mundane definition of the graduate worker as an apprentice first and foremost. Drawing on the public literature of the Committee on Rights and Compensation (CRC), a current effort to unionize graduate workers underway at the University of Colorado Boulder, I examine the ways in which the CRC is attempting to introduce previously hidden, novel definitions of the graduate worker as a professional first and foremost

Multi-filament structures in relativistic self-focusing

A simple model is derived to prove the multi-filament structure of relativistic self-focusing with ultra-intense lasers. Exact analytical solutions describing the transverse structure of waveguide channels with electron cavitation, for which both the relativistic and ponderomotive nonlinearities are taken into account, are presented.Comment: 21 pages, 12 figures, submitted to Physical Review

Electromagnetic energy penetration in the self-induced transparency regime of relativistic laser-plasma interactions

Two scenarios for the penetration of relativistically intense laser radiation into an overdense plasma, accessible by self-induced transparency, are presented. For supercritical densities less than 1.5 times the critical one, penetration of laser energy occurs by soliton-like structures moving into the plasma. At higher background densities laser light penetrates over a finite length only, that increases with the incident intensity. In this regime plasma-field structures represent alternating electron layers separated by about half a wavelength by depleted regions.Comment: 9 pages, 4 figures, submitted for publication to PR

Stability of narrow beams in bulk Kerr-type nonlinear media

We consider (2+1)-dimensional beams, whose transverse size may be comparable to or smaller than the carrier wavelength, on the basis of an extended version of the nonlinear Schr\"{o}dinger equation derived from the Maxwell`s equations. As this equation is very cumbersome, we also study, in parallel to it, its simplified version which keeps the most essential term: the term which accounts for the {\it nonlinear diffraction}. The full equation additionally includes terms generated by a deviation from the paraxial approximation and by a longitudinal electric-field component in the beam. Solitary-wave stationary solutions to both the full and simplified equations are found, treating the terms which modify the nonlinear Schr\"{o}dinger equation as perturbations. Within the framework of the perturbative approach, a conserved power of the beam is obtained in an explicit form. It is found that the nonlinear diffraction affects stationary beams much stronger than nonparaxiality and longitudinal field. Stability of the beams is directly tested by simulating the simplified equation, with initial configurations taken as predicted by the perturbation theory. The numerically generated solitary beams are always stable and never start to collapse, although they display periodic internal vibrations, whose amplitude decreases with the increase of the beam power.Comment: 7 pages, 6 figures Accepted for publication in PR

Academic Performance and Behavioral Patterns

Identifying the factors that influence academic performance is an essential part of educational research. Previous studies have documented the importance of personality traits, class attendance, and social network structure. Because most of these analyses were based on a single behavioral aspect and/or small sample sizes, there is currently no quantification of the interplay of these factors. Here, we study the academic performance among a cohort of 538 undergraduate students forming a single, densely connected social network. Our work is based on data collected using smartphones, which the students used as their primary phones for two years. The availability of multi-channel data from a single population allows us to directly compare the explanatory power of individual and social characteristics. We find that the most informative indicators of performance are based on social ties and that network indicators result in better model performance than individual characteristics (including both personality and class attendance). We confirm earlier findings that class attendance is the most important predictor among individual characteristics. Finally, our results suggest the presence of strong homophily and/or peer effects among university students

Intensive Wheat Management for Yield and Quality: The Role of Variety, Environment, and Management Practices

Management (M), variety (V), and environment (E) greatly influence wheat yield and quality. With the objective of determining the partial influence of V, E, and M, we conducted a field experiment where we imposed four management intensities to five wheat varieties during six site-years in Kansas and Oklahoma. Management intensities were 1) low-input (N fertility for a yield goal of 60 bu/a); 2) high-input (foliar fungi­cide, sulfur and chloride fertilizers, growth regulator, and nitrogen (N) fertility for a yield goal of 100 bu/a); 3) high-input minus fungicide; and 4) high-input minus addi­tional N. We selected commonly grown wheat varieties with contrasting yield potential and quality characteristics. We used a split-plot design with M as whole-plots (estab­lished in randomized complete block design), and V as sub-plot (completely random­ized within whole-plot). Variance component analyses suggested that E accounted for 63% of the variability in wheat yield and 55% of the variability in grain test weight; G accounted for 1 and 23% of the variability in yield and test weight, and M accounted for 1% of the variability of both. The interactions V × G and E × M accounted for 4 and 9% of the variability in yield, and 10 and 1% of the variability in test weight, respectively. Analysis of variance pooled across the entire dataset considering V and M fixed and E random suggested a significant G × M interaction on yield, which ranged from 49–61 bu/a. Meanwhile, both V and M affected test weight, which ranged from 52–58 lb/bu for the different V and from 55–57 lb/bu for the different M. These results suggest that E has the greatest impact in yield and quality, but there is room for yield improvement through V-specific M, and for quality improvement through V and M separately