Traffic Noise and Sexual Selection: Studies of Anthropogenic Impact on Bird Songs and Undergraduate Student Reasoning of Evolutionary Mechanisms

Humans have transformed much of the natural landscape and are continuing to do so at an accelerated rate, compromising natural areas that serve as important habitat for many species. Roads impact much of the environment as they fragment habitat and introduce traffic noise into the acoustic environment, deferentially affecting wildlife in roadside habitat. I explored how traffic noise affects the detection of birds based on whether their vocalizations were masked by traffic noise. Masked species detection was not affected by an increase in traffic noise amplitude, while there was a negative effect of traffic noise amplitude on unmasked species detection, an unexpected result. Conducting more experiments on individual species detection will help ecologists better understand the changes in behavior that influence detection. The effect of human activity on the environment should be better understood by more than just ecologists. Yet, people in the United States fall behind other developed countries in their understanding of many scientific processes, such as evolution. Improved evolutionary knowledge leads people to have a higher acceptance of evolution, and biology educators are responsible for improving evolution education to promote more acceptance. For example, biology students seem committed to survival-based reasoning of evolution, but there are other important evolutionary forces to consider, such as sexual selection. Multiple selection pressures can act on a species, including pressures that select for traits that are maladaptive for survival. Through interviews, we explored how selection for the same and different trait variants affected student reasoning of evolution. When asked to describe evolution in a scenario where selection favored the same variant of a trait, students relied on survival-based reasoning. When students were presented with a scenario where different selection pressures selected for different trait variants, most students described how sexual selection acted on the traits of the population and included reproductive potential as a component of fitness and inheritance in their descriptions of evolution. Teaching examples with scenarios where different selection pressures are selecting for different traits may improve student ability to reason about the role of sexual selection in evolution and the role of reproductive potential in fitness, improving overall understanding of evolution. Advisor: Joseph T. Daue

Traffic Noise and Sexual Selection: Studies of Anthropogenic Impact on Bird Songs and Undergraduate Student Reasoning of Evolutionary Mechanisms

Humans have transformed much of the natural landscape and are continuing to do so at an accelerated rate, compromising natural areas that serve as important habitat for many species. Roads impact much of the environment as they fragment habitat and introduce traffic noise into the acoustic environment, deferentially affecting wildlife in roadside habitat. I explored how traffic noise affects the detection of birds based on whether their vocalizations were masked by traffic noise. Masked species detection was not affected by an increase in traffic noise amplitude, while there was a negative effect of traffic noise amplitude on unmasked species detection, an unexpected result. Conducting more experiments on individual species detection will help ecologists better understand the changes in behavior that influence detection. The effect of human activity on the environment should be better understood by more than just ecologists. Yet, people in the United States fall behind other developed countries in their understanding of many scientific processes, such as evolution. Improved evolutionary knowledge leads people to have a higher acceptance of evolution, and biology educators are responsible for improving evolution education to promote more acceptance. For example, biology students seem committed to survival-based reasoning of evolution, but there are other important evolutionary forces to consider, such as sexual selection. Multiple selection pressures can act on a species, including pressures that select for traits that are maladaptive for survival. Through interviews, we explored how selection for the same and different trait variants affected student reasoning of evolution. When asked to describe evolution in a scenario where selection favored the same variant of a trait, students relied on survival-based reasoning. When students were presented with a scenario where different selection pressures selected for different trait variants, most students described how sexual selection acted on the traits of the population and included reproductive potential as a component of fitness and inheritance in their descriptions of evolution. Teaching examples with scenarios where different selection pressures are selecting for different traits may improve student ability to reason about the role of sexual selection in evolution and the role of reproductive potential in fitness, improving overall understanding of evolution. Advisor: Joseph T. Daue

Sexual Selection as a Tool to Improve Student Reasoning of Evolution

There is an emphasis on survival-based selection in biology education that can allow students to neglect other important evolutionary components, such as sexual selection, reproduction, and inheritance. Student understanding of the role of reproduction in evolution is as important as student understanding of the role of survival. Limiting instruction to survival- based scenarios (e.g., effect of food on Galapagos finch beak shape) may not provide students with enough context to guide them to complete evolutionary reasoning. Different selection forces can work in concert or oppose one another, and sexual selection can lead to the selection of trait variants that are maladaptive for survival. In semistructured interviews with undergraduate biology students (n = 12), we explored how leading students through a sequence of examples affected student reasoning of evolution. When presented with an example where sexual selection and survivability favored the same variant of a trait, students emphasized survival in their reasoning. When presented with a scenario where sexual selection selected for trait variants that were maladaptive for survival, more students described how two different selection forces contributed to evolutionary outcomes and described reproductive potential as a part of fitness. Moreover, these students considered how the maladaptive traits were inherited in the population. Scenarios where sexual selection and survival-based selection were opposed improved student ability to reason about how factors other than survival impact evolutionary change. When instructors introduce students to scenarios where survival-based selection and sexual selection are opposed, they allow students to change their reasoning toward inclusion of reproduction in their evolutionary reasoning

An efficient and high-throughput approach for experimental validation of novel human gene predictions

AbstractA highly automated RT-PCR-based approach has been established to validate novel human gene predictions with no prior experimental evidence of mRNA splicing (ab initio predictions). Ab initio gene predictions were selected for high-throughput validation using predicted protein classification, sequence similarity to other genomes, colocalization with an MPSS tag, or microarray expression. Initial microarray prioritization followed by RT-PCR validation was the most efficient combination, resulting in approximately 35% of the ab initio predictions being validated by RT-PCR. Of the 7252 novel genes that were prioritized and processed, 796 constituted real transcripts. In addition, high-throughput RACE successfully extended the 5′ and/or 3′ ends of >60% of RT-PCR-validated genes. Reevaluation of these transcripts produced 574 novel transcripts using RefSeq as a reference. RT-PCR sequencing in combination with RACE on ab initio gene predictions could be used to define the transcriptome across all species

Temporal changes in clinical and radiographic variables in dogs with preclinical myxomatous mitral valve disease: The EPIC study

The Evaluation of pimobendan in dogs with cardiomegaly caused by preclinical myxomatous mitral valve disease (EPIC) study monitored dogs with myxomatous mitral valve disease (MMVD) as they developed congestive heart failure (CHF)

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Traffic Noise and Sexual Selection: Studies of Anthropogenic Impact on Bird Songs and Undergraduate Student Reasoning of Evolutionary Mechanisms

Humans have transformed much of the natural landscape and are continuing to do so at an accelerated rate, compromising natural areas that serve as important habitat for many species. Roads impact much of the environment as they fragment habitat and introduce traffic noise into the acoustic environment, deferentially affecting wildlife in roadside habitat. I explored how traffic noise affects the detection of birds based on whether their vocalizations were masked by traffic noise. Masked species detection was not affected by an increase in traffic noise amplitude, while there was a negative effect of traffic noise amplitude on unmasked species detection, an unexpected result. Conducting more experiments on individual species detection will help ecologists better understand the changes in behavior that influence detection. The effect of human activity on the environment should be better understood by more than just ecologists. Yet, people in the United States fall behind other developed countries in their understanding of many scientific processes, such as evolution. Improved evolutionary knowledge leads people to have a higher acceptance of evolution, and biology educators are responsible for improving evolution education to promote more acceptance. For example, biology students seem committed to survival-based reasoning of evolution, but there are other important evolutionary forces to consider, such as sexual selection. Multiple selection pressures can act on a species, including pressures that select for traits that are maladaptive for survival. Through interviews, we explored how selection for the same and different trait variants affected student reasoning of evolution. When asked to describe evolution in a scenario where selection favored the same variant of a trait, students relied on survival-based reasoning. When students were presented with a scenario where different selection pressures selected for different trait variants, most students described how sexual selection acted on the traits of the population and included reproductive potential as a component of fitness and inheritance in their descriptions of evolution. Teaching examples with scenarios where different selection pressures are selecting for different traits may improve student ability to reason about the role of sexual selection in evolution and the role of reproductive potential in fitness, improving overall understanding of evolution. Advisor: Joseph T. Daue

Assessing Evolutionary Reasoning of Introductory Biology Students

Question: Does proficiency in natural selection knowledge predict the quality of student reasoning of reproductive potential as a component of fitness? Hypothesis: Students with higher scores on the Concept Inventory of Natural Selection (CINS) will have more accurate descriptions of reproductive potential as a part of fitness. Goals: Assess student ability to reason about fitness and selection in a variety of contexts. Assess student reasoning of evolutionary implications of an ecological scenari

The Effects of Urbanization on Fear in Wildlife

Through this study we sought out to determine if Fox Squirrels in Lincoln, Nebraska exhibited a change in response to aerial versus terrestrial predators in urban areas. We addressed the possible consequences that human disturbance has on daily stimuli, predator behaviors, and, in turn, prey behaviors. Specifically, the experiment exposed Fox Squirrels to the vocalizations and visual models of an aerial predator, terrestrial predator, and a control species. Squirrels did not show a significant change in behavior between predator types. However, fox squirrels displayed correct anti-predator behaviors by only responding to the predators and not the control. The time it took to respond, length of response, and flee distance were not distinguishable by predator type