Micro-evolutionary potential of temperature dependent sex determination in a wild population of painted turtles, Chrysemys picta

The ways in which organisms determine sex are diverse. Sex determination systems are important because of the effect they have on sex ratios within a population, which affects reproductive success, levels of inbreeding, and population viability. In environmental sex determination (ESD), sex is determined in response to immediate environmental factors after conception. A common form of ESD in non-avian reptiles and some fish is temperature-dependant sex determination (TSD). Individual sex is determined by the temperature during the middle one-third of embryonic development, and the threshold between male and female development is often over a very small (\u3c 2yC) range. While this form of sex determination has been maintained in a species or population over millions of years, TSD species may experience drastic skews in sex ratio in response to large climatic upheavals. Theoretically, response to selection for the rarer sex may produce evolutionary change at two levels in reptiles: 1) maternal nesting behavior with respect to thermal conditions and 2) thermal sensitivity of the threshold between male and female development. The results from this dissertation reveal that both onset of nesting and nest-site vegetation cover have low heritability and thus low potential to respond to selection. Nesting behavior is dependent on the winter preceding the nesting season, however, and environment-specific analyses suggest that additive genetic variance increases for onset of nesting after warmer winters and increases for vegetation cover over the nest after cold winters. As a result, heritability may be dependent on the winter preceding the nesting season in this system. Estimates of repeatability corroborate these results. There is a significant, genetic-based tendency for turtles to nest in areas with minimal vegetation cover after colder winters, while there is a significant, genetic basis for earlier first nesting dates after warmer winters. Genetic correlations between warmer and colder winters for vegetation cover are very high and suggest that no potential genotype-by-environment (G y E) interaction exists, while potential G y E between winter environments for first nesting date between winter environments is inconclusive. Threshold temperatures may respond to selection for sex ratio biases as well. Maternal half-sib analysis facilitated by natural multiple paternity suggests that family effects on hatchling sex in TSD species are not exclusively driven by maternal effects and that there is a detectable genetic variance of the sire. Thus, the sex determination pathway\u27s sensitivity to temperature (i.e. primary sex ratio) may evolve in response to sex-ratio selection. The effective heritability, which predicts the relative rate of change of threshold temperature, was estimated to be 0.11, while the effective heritability of nesting behavior was estimated to be 0.079. Since sire genetic variance can substantially influence the sex of offspring when the clutch is incubated at temperatures that produce both sexes, mating with multiple males may have a homogenizing effect on sex ratio variance within and between nests. No significant reduction in sex ratio variance for multiple paternity clutches was observed in the study presented here, but theoretically TSD may provide an ideal situation for bet-hedging. Clutches with multiple sires had higher hatching success rate and lower variance for hatching relative to clutches with a single sire. The incidence of multiply sired clutches increased with plastron length (a proxy for age), although there was no significant interaction between fitness, plastron length, and multiple paternity. In conclusion, these studies suggest that temperature dependent sex determination may respond to selection from sex ratio biases either through threshold temperature or nesting behavior, but both are likely to respond to selection slowly. Further, multiple paternity does not seem to homogenize sex ratios between clutches for the population examined here; however, additional studies are needed to exclude possible confounding factors

Field-measured heritability of the threshold for sex determination in a turtle with temperature-dependent sex determination

Problem: For temperature-dependent sex determination to respond to selection, there should be genetic variance underlying the threshold that switches development from a male-producing program to a female-producing program. Genetic variance for this threshold in reptiles has never been estimated under field conditions. Methods: We estimated variance components of the thermal sensitivity of the sex determination threshold under field conditions for the painted turtle, Chrysemys picta, a species that has temperature-dependent sex determination. Multiple paternity within clutches was identified by genotyping females and their offspring. We endeavoured to statistically account for common nest and maternal effects and estimated the genetic variance underlying the sex determination threshold under field conditions by isolating the contribution of sires within a single clutch. Results: With 51 clutches containing 393 offspring, we estimated significant heritability for the sex determination threshold (h2 = 0.351, 95% CI = [0.164, 0.832]). Using a more restrictive dataset, which included only those clutches where each sire was represented by at least two offspring (34 nests, 273 hatchlings), heritability was not significantly different from zero (h2 = 0.173, 95% CI = [0.000, 0.628]). Paternal siring success did not influence hatchling sex; thus, we have no evidence to support differential sex allocation across different sires within the same nest. Conclusion: We used a natural ‘breeding design’ under field conditions to show that the threshold of temperature-dependent sex determination may have a heritable genetic basis

Contrasting patterns of rapid molecular evolution within the p53 network across mammal and sauropsid lineages

Cancer is a threat to multicellular organisms, yet the molecular evolution of pathways that prevent the accumulation of genetic damage has been largely unexplored. The p53 network regulates how cells respond to DNA-damaging stressors. While there has been research on the p53 gene and the transcription factors it encodes, we know little about p53 network regulation. In this study, we performed comparative genetic analyses of the p53 network to quantify the number of genes within the network that are rapidly evolving and constrained, and the association between lifespan and the patterns of evolution. Based on our previous published dataset, we used genomes and transcriptomes of 34 sauropsids and 32 mammals to analyze the molecular evolution of 45 genes within the p53 network. We found that genes in the network exhibited evidence of positive selection and divergent molecular evolution in mammals and sauropsids. Specifically, we found more evidence of positive selection in sauropsids than mammals, indicating that sauropsids have different targets of selection. In sauropsids, more genes upstream in the network exhibited positive selection, and this observation is driven by positive selection in squamates, which is consistent with previous work showing rapid divergence and adaptation of metabolic and stress pathways in this group. Finally, we identified a negative correlation between maximum lifespan and the number of genes with evidence of divergent molecular evolution, indicating that species with longer lifespans likely experienced less variation in selection across the network. In summary, our study offers evidence that comparative genomic approaches can provide insights into how molecular networks have evolved across diverse species

Galaxy Selection and Clustering and Lyman alpha Absorber Identification

The effects of galaxy selection on our ability to constrain the nature of weak Ly\alpha absorbers at low redshift are explored. Current observations indicate the existence of a population of gas-rich, low surface brightness (LSB) galaxies, and these galaxies may have large cross sections for Ly\alpha absorption. Absorption arising in LSB galaxies may be attributed to HSB galaxies at larger impact parameters from quasar lines of sight, so that the observed absorption cross sections of galaxies may seem unreasonably large. Thus it is not possible to rule out scenarios where LSB galaxies make substantial contributions to Ly\alpha absorption using direct observations. Less direct tests, where observational selection effects are taken into account using simulations, should make it possible to determine the nature of Ly\alpha absorbers by observing a sample of ~100 galaxies around quasar lines of sight with well-defined selection criteria. Such tests, which involve comparing simulated and observed plots of the unidentified absorber fractions and absorbing galaxy fractions versus impact parameter, can distinguish between scenarios where absorbers arise in particular galaxies and those where absorbers arise in gas tracing the large scale galaxy distribution. Care must be taken to minimize selection effects even when using these tests. Results from such tests are likely to depend upon the limiting neutral hydrogen column density. While not enough data are currently available to make a strong conclusion about the nature of moderately weak absorbers, evidence is seen that such absorbers arise in gas that is around or between galaxies that are often not detected in surveys.Comment: 15 pages, 10 figures, accepted to the Astrophysical Journa

Comparing Galaxies and Lyman Alpha Absorbers at Low Redshift

A scenario is explored in which Lyman alpha absorbers at low redshift arise from lines of sight through extended galaxy disks, including those of dwarf and low surface brightness galaxies. A population of galaxies is simulated based upon observed distributions of galaxy properties, and the gas disks are modeled using pressure and gravity confinement. Some parameter values are ruled out by comparing simulation results with the observed galaxy luminosity function, and constraints may be made on the absorbing cross sections of galaxies. Simulation results indicate that it is difficult to match absorbers with particular galaxies observationally since absorption typically occurs at high impact parameters (>200 kpc) from luminous galaxies. Low impact parameter absorption is dominated by low luminosity dwarfs. A large fraction of absorption lines is found to originate from low surface brightness galaxies, so that the absorbing galaxy is likely to be misidentified. Low redshift Lyman alpha absorber counts can easily be explained by moderately extended galaxy disks when low surface brightness galaxies are included, and it is easily possible to find a scenario which is consistent with observed the galaxy luminosity function, with low redshift Lyman limit absorber counts, and with standard nucleosynthesis predictions of the baryon density, Omega_Baryon.Comment: 17 pages, 8 figures, accepted to the Astrophysical Journa

Smaller classes promote equitable student participation in STEM

Under embargo until: 2020-07-24As science, technology, engineering, and mathematics (STEM) classrooms in higher education transition from lecturing to active learning, the frequency of student interactions in class increases. Previous research documents a gender bias in participation, with women participating less than would be expected on the basis of their numeric proportions. In the present study, we asked which attributes of the learning environment contribute to decreased female participation: the abundance of in-class interactions, the diversity of interactions, the proportion of women in class, the instructor's gender, the class size, and whether the course targeted lower division (first and second year) or upper division (third or fourth year) students. We calculated likelihood ratios of female participation from over 5300 student–instructor interactions observed across multiple institutions. We falsified several alternative hypotheses and demonstrate that increasing class size has the largest negative effect. We also found that when the instructors used a diverse range of teaching strategies, the women were more likely to participate after small-group discussions.acceptedVersio

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders

Micro-evolutionary potential of temperature dependent sex determination in a wild population of painted turtles, Chrysemys picta

The ways in which organisms determine sex are diverse. Sex determination systems are important because of the effect they have on sex ratios within a population, which affects reproductive success, levels of inbreeding, and population viability. In environmental sex determination (ESD), sex is determined in response to immediate environmental factors after conception. A common form of ESD in non-avian reptiles and some fish is temperature-dependant sex determination (TSD). Individual sex is determined by the temperature during the middle one-third of embryonic development, and the threshold between male and female development is often over a very small ( The results from this dissertation reveal that both onset of nesting and nest-site vegetation cover have low heritability and thus low potential to respond to selection. Nesting behavior is dependent on the winter preceding the nesting season, however, and environment-specific analyses suggest that additive genetic variance increases for onset of nesting after warmer winters and increases for vegetation cover over the nest after cold winters. As a result, heritability may be dependent on the winter preceding the nesting season in this system. Estimates of repeatability corroborate these results. There is a significant, genetic-based tendency for turtles to nest in areas with minimal vegetation cover after colder winters, while there is a significant, genetic basis for earlier first nesting dates after warmer winters. Genetic correlations between warmer and colder winters for vegetation cover are very high and suggest that no potential genotype-by-environment (G y E) interaction exists, while potential G y E between winter environments for first nesting date between winter environments is inconclusive. Threshold temperatures may respond to selection for sex ratio biases as well. Maternal half-sib analysis facilitated by natural multiple paternity suggests that family effects on hatchling sex in TSD species are not exclusively driven by maternal effects and that there is a detectable genetic variance of the sire. Thus, the sex determination pathway's sensitivity to temperature (i.e. primary sex ratio) may evolve in response to sex-ratio selection. The effective heritability, which predicts the relative rate of change of threshold temperature, was estimated to be 0.11, while the effective heritability of nesting behavior was estimated to be 0.079. Since sire genetic variance can substantially influence the sex of offspring when the clutch is incubated at temperatures that produce both sexes, mating with multiple males may have a homogenizing effect on sex ratio variance within and between nests. No significant reduction in sex ratio variance for multiple paternity clutches was observed in the study presented here, but theoretically TSD may provide an ideal situation for bet-hedging. Clutches with multiple sires had higher hatching success rate and lower variance for hatching relative to clutches with a single sire. The incidence of multiply sired clutches increased with plastron length (a proxy for age), although there was no significant interaction between fitness, plastron length, and multiple paternity. In conclusion, these studies suggest that temperature dependent sex determination may respond to selection from sex ratio biases either through threshold temperature or nesting behavior, but both are likely to respond to selection slowly. Further, multiple paternity does not seem to homogenize sex ratios between clutches for the population examined here; however, additional studies are needed to exclude possible confounding factors.</p