EVOLUTION, DEVELOPMENT, AND GENETICS OF OPSIN GENE EXPRESSION IN AFRICAN CICHLID FISHES

The molecular genetic mechanisms that underlie phenotypic evolution include mutations within protein-coding, cis-regulatory, and trans-regulatory factors. Although many studies have examined how these mutations individually contribute to phenotypic divergence and the formation of new species, none have examined how they may do so collectively. In this study, I examine how these molecular genetic mutations collectively contribute to the evolution of color vision among African cichlid fishes. I show that phenotypic divergence in cichlid color vision is achieved by mutations affecting the coding sequence and expression of seven opsin genes. After contrasting the roles of these two mechanisms, I use bioinformatic-, association-, and experimental genetic analyses to determine what role mutations in cis- and trans-regulatory DNA play in the evolution of cichlid opsin expression. Specifically, I demonstrate that: (1) Protein-coding mutations primarily affect cichlid opsins sensitive to the ends of the visible light spectrum (SWS1 [ultraviolet-sensitive] and LWS [red-sensitive]). (2) Changes in opsin gene expression contribute to large differences in color vision among closely related species. These analyses also reveal that the expression of the SWS1 and SWS2B opsins have diverged among closely related cichlids in association with foraging preferences and ambient light intensity, suggesting that their expression has evolved due to natural selection. Ancestral state reconstructions reveal that changes in opsin expression have evolved repeatedly among cichlids in Lakes Tanganyika and Malawi; further, I find that this repeated evolution has likely been achieved by repeated changes to cichlid development. (3) Bioinformatic analyses suggest that cichlids have diverged in multiple cis-regulatory sequences surrounding the opsin genes, and association mapping identified three putative single nucleotide polymorphisms upstream of the SWS2A (blue), RH2B (blue-green), and LWS (red) opsins that may contribute to cichlid opsin expression differences in cis. (4) Genetic mapping in experimental crosses suggests that divergence in multiple trans-regulatory factors also contribute to the evolution of SWS2B (violet), RH2A (green), and LWS (red) opsin expression. The contribution of these trans-regulatory factors to the evolution of cichlid opsin expression may outweigh those in cis. These results reveal that multiple molecular genetic mechanisms can contribute to phenotypic evolution among closely related species

Changes in Belize Coral Reef Bivalve Assemblages Over Time Contradicts What is Seen in Panama

Caribbean coral reef ecosystem health has drastically declined since large-scale monitoring began in the 1970s, due to local human stressors and climate change. However, we know less about anthropogenic change on Caribbean reefs before monitoring began. Reef sediment cores can help provide context for understanding the causes and consequences of changes in reef ecosystems as they can provide a millennial-scale record of reef communities and environments. For example, reef sediment cores from Panama suggest that coral reef decline began as early as the 18th century and was closely linked to land use change. We utilized bivalve subfossils preserved within a 3.5m-long sediment core collected from a lagoonal reef in central Belize to track changes in reef environmental conditions from the early 1500s to the late 1930s. In the bottom of the core, dating to 1516, the percent of infaunal bivalves is 0.48%. In the top of the core, dating to 1938, the percent of infaunal bivalves increased to 39.13%. The increase of infaunal bivalve species suggests a loss of hard substrate in the reef ecosystem. This trend has been observed in other places around the Caribbean, and suggests a loss in coral reef substrate, possibly due to changes in water quality and/or a loss of reef herbivory from fishing. This later loss is contrasting what is seen in Panama, where there is loss as early as the 1700s.Smithsonian InstitutionUniversity of California: San DiegoNo embargoAcademic Major: Earth Science

Amotivation: A Key Predictor of College GPA, College Match, and First-Year Retention

Two studies examined the relationships between motivational orientation, college student success, and first-year retention.  In Study 1, 523 college students completed measures of motivational orientation and student success.  Results indicated that intrinsic and extrinsic motivation were positively related to college GPA, student-university match and adjustment to college. In contrast, amotivation was negatively related to these dependent variables. Study 2 examined a mediational model in which motivational orientation, most consistently amotivation, predicted lower college student GPA and poorer college match. These, in turn predicted a decrease in first-to-second-year retention among 385 first-year college students. These results suggest that colleges may wish to address amotivation among students as a way to enhance student success and retention.

The Genetic Basis of Pigment Pattern Differentiation in Lake Malawi African Cichlids

The cichlids of East Africa are a well-known group of fishes that display a wide range of phenotypic diversity, including differences in tooth shape, facial and body morphology, visual palettes, and body coloration. This diversity in phenotype was generated within the last 10 million years via an adaptive radiation. The cichlids of Lake Malawi are particularly known for their wide variation in male color patterns, which is thought to have been driven by sexual selection. Given their recent evolution, different species of cichlids can be intercrossed in the lab to identify the underlying genetic basis of phenotypic traits via a forward genetics approach. Using this methodology, I created a hybrid cross between two cichlid species, Metriaclima zebra and M. mbenjii that differ in several pigmentation traits in an attempt to identify the underlying genetic basis of these traits. After quantifying these pigmentation traits, I was able to use the Castle-Wright equation to estimate that a small number of genes underlie these traits. I was then able to identify quantitative trait loci (QTL) for three traits, dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. The QTL for dorsal and caudal fin xanthophores were found to overlap on the same linkage group. I was able to identify and preliminarily analyze the candidate gene, AAK1, for this shared QTL region. In addition to this pigmentation work, I was also able to identify a genomic region where a potential XY sex determiner is located and analyze a candidate gene, GSDF

The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity

Differential gene expression and coding sequence evolution play complementary roles in the adaptive diversification of cichlid sensory systems

Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish

Background How and why animals lose eyesight during adaptation to the dark and food-limited cave environment has puzzled biologists since the time of Darwin. More recently, several different adaptive hypotheses have been proposed to explain eye degeneration based on studies in the teleost Astyanax mexicanus, which consists of blind cave-dwelling (cavefish) and sighted surface-dwelling (surface fish) forms. One of these hypotheses is that eye regression is the result of indirect selection for constructive characters that are negatively linked to eye development through the pleiotropic effects of Sonic Hedgehog (SHH) signaling. However, subsequent genetic analyses suggested that other mechanisms also contribute to eye regression in Astyanax cavefish. Here, we introduce a new approach to this problem by investigating the phenotypic and genetic relationships between a suite of non-visual constructive traits and eye regression. Results Using quantitative genetic analysis of crosses between surface fish, the Pachón cavefish population and their hybrid progeny, we show that the adaptive vibration attraction behavior (VAB) and its sensory receptors, superficial neuromasts (SN) specifically found within the cavefish eye orbit (EO), are genetically correlated with reduced eye size. The quantitative trait loci (QTL) for these three traits form two clusters of congruent or overlapping QTL on Astyanax linkage groups (LG) 2 and 17, but not at the shh locus on LG 13. Ablation of EO SN in cavefish demonstrated a major role for these sensory receptors in VAB expression. Furthermore, experimental induction of eye regression in surface fish via shh overexpression showed that the absence of eyes was insufficient to promote the appearance of VAB or EO SN. Conclusions We conclude that natural selection for the enhancement of VAB and EO SN indirectly promotes eye regression in the Pachón cavefish population through an antagonistic relationship involving genetic linkage or pleiotropy among the genetic factors underlying these traits. This study demonstrates a trade-off between the evolution of a non-visual sensory system and eye regression during the adaptive evolution of Astyanax to the cave environment

Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation

Citation: Husemann, M., Tobler, M., McCauley, C., Ding, B., & Danley, P. D. (2017). Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation. Ecology and Evolution. doi:10.1002/ece3.2823Phenotypic differences may have genetic and plastic components. Here, we investigated the contributions of both for differences in body shape in two species of Lake Malawi cichlids using wild-caught specimens and a common garden experiment. We further hybridized the two species to investigate the mode of gene action influencing body shape differences and to examine the potential for transgressive segregation. We found that body shape differences between the two species observed in the field are maintained after more than 10 generations in a standardized environment. Nonetheless, both species experienced similar changes in the laboratory environment. Our hybrid cross experiment confirmed that substantial variation in body shape appears to be genetically determined. The data further suggest that the underlying mode of gene action is complex and cannot be explained by simple additive or additive-dominance models. Transgressive phenotypes were found in the hybrid generations, as hybrids occupied significantly more morphospace than both parentals combined. Further, the body shapes of transgressive individuals resemble the body shapes observed in other Lake Malawi rock-dwelling genera. Our findings indicate that body shape can respond to selection immediately, through plasticity, and over longer timescales through adaptation. In addition, our results suggest that hybridization may have played an important role in the diversification of Lake Malawi cichlids through creating new phenotypic variation. © 2017 Published by John Wiley & Sons Ltd

Structure-Function Analysis of Diacylglycerol Acyltransferase Sequences from 70 Organisms

<p>Abstract</p> <p>Background</p> <p>Diacylglycerol acyltransferase families (DGATs) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. Understanding the roles of DGATs will help to create transgenic plants with value-added properties and provide clues for therapeutic intervention for obesity and related diseases. The objective of this analysis was to identify conserved sequence motifs and amino acid residues for better understanding of the structure-function relationship of these important enzymes.</p> <p>Results</p> <p>117 DGAT sequences from 70 organisms including plants, animals, fungi and human are obtained from database search using tung tree DGATs. Phylogenetic analysis separates these proteins into DGAT1 and DGAT2 subfamilies. These DGATs are integral membrane proteins with more than 40% of the total amino acid residues being hydrophobic. They have similar properties and amino acid composition except that DGAT1s are approximately 20 kDa larger than DGAT2s. DGAT1s and DGAT2s have 41 and 16 completely conserved amino acid residues, respectively, although only two of them are shared by all DGATs. These residues are distributed in 7 and 6 sequence blocks for DGAT1s and DGAT2s, respectively, and located at the carboxyl termini, suggesting the location of the catalytic domains. These conserved sequence blocks do not contain the putative neutral lipid-binding domain, mitochondrial targeting signal, or ER retrieval motif. The importance of conserved residues has been demonstrated by site-directed and natural mutants.</p> <p>Conclusions</p> <p>This study has identified conserved sequence motifs and amino acid residues in all 117 DGATs and the two subfamilies. None of the completely conserved residues in DGAT1s and DGAT2s is present in recently reported isoforms in the multiple sequences alignment, raising an important question how proteins with completely different amino acid sequences could perform the same biochemical reaction. The sequence analysis should facilitate studying the structure-function relationship of DGATs with the ultimate goal to identify critical amino acid residues for engineering superb enzymes in metabolic engineering and selecting enzyme inhibitors in therapeutic application for obesity and related diseases.</p

Teaching Creativity in Engineering Courses

Background The ability to engage in a creative process to solve a problem or to design a novel artifact is essential to engineering as a profession. Research indicates a need for curricula that enhance students' creative skills in engineering. Purpose Our purpose was to document current practices in engineering pedagogy with regard to opportunities for students' creative growth by examining learning goals, instructional methods, and assessments focused on cognitive creative skills. Design/Method We conducted a critical case study of engineering pedagogy at a single university with seven engineering courses where instructors stated the goal of fostering creativity. Data included instructor and student interviews, student surveys, and course materials. For qualitative analysis, we used frameworks by Treffinger, Young, Selby, and Shepardson and by Wiggins and McTighe. Results One aspect of creativity, convergent thinking (including analysis and evaluation), was well represented in the engineering courses in our case study. However, instruction on generating ideas and openness to exploring ideas was less often evident. For many of the creative skills, especially those related to divergent thinking and idea exploration, assessments were lacking. Conclusions An analysis of pedagogy focused on goals, instruction, and assessments in the engineering curriculum revealed opportunities for growth in students' creative skill development. Designing assessments that motivate students to improve their creative skills and to become more aware of their own creative process is a key need in engineering pedagogy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108079/1/jee20048.pd