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"Anderson, Eric C."
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Uncharted : Lewis and Clark in Arcane America
\"High adventure on the frontier of muskets and magic!\"--Jacket.
Book
Affective Beliefs Influence the Experience of Eating Meat
People believe they experience the world objectively, but research continually demonstrates that beliefs influence perception. Emerging research indicates that beliefs influence the experience of eating. In three studies, we test whether beliefs about how animals are raised can influence the experience of eating meat. Samples of meat were paired with descriptions of animals raised on factory farms or raised on humane farms. Importantly, the meat samples in both conditions were identical. However, participants experienced the samples differently: meat paired with factory farm descriptions looked, smelled, and tasted less pleasant. Even basic properties of flavor were influenced: factory farmed samples tasted more salty and greasy. Finally, actual behavior was influenced: participants consumed less when samples were paired with factory farm descriptions. These findings demonstrate that the experience of eating is not determined solely by physical properties of stimuli-beliefs also shape experience.
Journal Article
Sex-dependent dominance maintains migration supergene in rainbow trout
Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (
Oncorhynchus mykiss
) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.
This study reveals sex-dependent dominance reversal across a large autosomal supergene in the rainbow trout, a mechanism for the resolution of sexual conflict in a species that lacks differentiated sex chromosomes.
Journal Article
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data
Low‐coverage whole‐genome sequencing (WGS) is increasingly used for the study of evolution and ecology in both model and non‐model organisms; however, effective application of low‐coverage WGS data requires the implementation of probabilistic frameworks to account for the uncertainties in genotype likelihoods. Here, we present a probabilistic framework for using genotype likelihoods for standard population assignment applications. Additionally, we derive the Fisher information for allele frequency from genotype likelihoods and use that to describe a novel metric, the effective sample size, which figures heavily in assignment accuracy. We make these developments available for application through WGSassign, an open‐source software package that is computationally efficient for working with whole‐genome data. Using simulated and empirical data sets, we demonstrate the behaviour of our assignment method across a range of population structures, sample sizes and read depths. Through these results, we show that WGSassign can provide highly accurate assignment, even for samples with low average read depths (<0.01X) and among weakly differentiated populations. Our simulation results highlight the importance of equalizing the effective sample sizes among source populations in order to achieve accurate population assignment with low‐coverage WGS data. We further provide study design recommendations for population assignment studies and discuss the broad utility of effective sample size for studies using low‐coverage WGS data.
Journal Article
Longitudinal idiographic assessment of adolescent-dog relationships and adaptive coping for youth with social anxiety: The Teen & Dog Study protocol
The Teen & Dog Study is a longitudinal research project aimed at understanding the impact of youth-dog relationships on youth coping with social anxiety. The study will follow 514 United States adolescents (ages 13–17) with high social anxiety who live with dogs and their families, collecting longitudinal assessments of their physiological, emotional, and social well-being. With a focus on identifying the mechanisms by which youth-dog interactions may support adaptive coping, the study has three primary aims: (1) assess how the youth-dog relationship contributes to coping with social anxiety over time, factoring in individual, family, and peer influences; (2) investigate family-level processes that enhance youth-dog relationships and identify barriers to optimization; and (3) examine how dog interactions influence adolescents’ physiological responses, particularly in relation to anxiety. The study integrates quantitative and qualitative data, including surveys, interviews, ecological momentary activity, and continuous physiological monitoring, to assess strategies for optimizing youth-dog interactions in the context of social anxiety. This paper outlines the study protocol and presents characteristics of the study sample at baseline. Ultimately, the Teen & Dog Study seeks to inform interventions that harness the benefits of youth-dog relationships to improve mental health outcomes.
Journal Article
The Power of Single-Nucleotide Polymorphisms for Large-Scale Parentage Inference
Likelihood-based parentage inference depends on the distribution of a likelihood-ratio statistic, which, in most cases of interest, cannot be exactly determined, but only approximated by Monte Carlo simulation. We provide importance-sampling algorithms for efficiently approximating very small tail probabilities in the distribution of the likelihood-ratio statistic. These importance-sampling methods allow the estimation of small false-positive rates and hence permit likelihood-based inference of parentage in large studies involving a great number of potential parents and many potential offspring. We investigate the performance of these importance-sampling algorithms in the context of parentage inference using single-nucleotide polymorphism (SNP) data and find that they may accelerate the computation of tail probabilities >1 millionfold. We subsequently use the importance-sampling algorithms to calculate the power available with SNPs for large-scale parentage studies, paying particular attention to the effect of genotyping errors and the occurrence of related individuals among the members of the putative mother–father–offspring trios. These simulations show that 60–100 SNPs may allow accurate pedigree reconstruction, even in situations involving thousands of potential mothers, fathers, and offspring. In addition, we compare the power of exclusion-based parentage inference to that of the likelihood-based method. Likelihood-based inference is much more powerful under many conditions; exclusion-based inference would require 40% more SNP loci to achieve the same accuracy as the likelihood-based approach in one common scenario. Our results demonstrate that SNPs are a powerful tool for parentage inference in large managed and/or natural populations.
Journal Article
Recent advances in conservation and population genomics data analysis
New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.
Journal Article
Bayesian inference of species hybrids using multilocus dominant genetic markers
Neutral genetic markers are useful for identifying species hybrids in natural populations, especially when used in conjunction with statistical methods like the one implemented in the software NewHybrids. Here, a short description of the extension of NewHybrids to dominant markers is given. Subsequently, an extensive series of simulations of amplified fragment length polymorphism (AFLP) data is performed to evaluate the prospects for hybrid identification with (possibly non-diagnostic) dominant markers. Distinguishing between F1's and F2's is shown to be difficult, possibly requiring upwards of 100 AFLP markers to be done accurately. Discriminating between pure-bred and non-pure (hybrid) individuals, however, is shown to be much easier, requiring perhaps as few as 10 dominant markers, even from relatively weakly diverged species.
Journal Article
Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead
Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.
Journal Article
“If I have any problems, I just want to see my primary care doctor”: perspectives on a proposed collaborative RUral PALliative care intervention (RuPal)
Background
People living with advanced heart failure in rural areas have poorer quality of care as their disease progresses, which may be due to lack of access to specialty palliative care. A collaborative care model, connecting specialty palliative care clinicians to embedded complex care teams in primary care practices, may increase access to palliative care in this population.
Research objectives
To explore perspectives on a proposed collaborative palliative care intervention and whether this intervention would be appropriate for people living with heart failure in rural areas.
Methods
We conducted a qualitative study (
n=
26), including patients with heart failure (
n=
7), caregivers (
n=
2), complex care team members working in primary care practices (
n=
5), primary care providers (
n=
5), interdisciplinary specialty palliative care clinicians (
n=
4), and cardiologists (
n=
3) all living and/or practicing in a rural community in Maine. Interviews were audio recorded and professionally transcribed. We used Max-QDA, line-by-line coding, and grounded theory analysis.
Results
We found people living and working in rural areas wanted palliative care integrated into primary care. Participants voiced suspicion about care “from outsiders” and that introduction of a specialty palliative care team into their medical care might not be well received. As one primary care provider noted “rural [people] are less influenced by … seeing the latest specialist,” so describing palliative care as a specialty may not be appealing. However, participants felt that patients would be open to receiving palliative care delivered by their primary care teams. Palliative care specialists and primary care clinical staff were enthusiastic about a collaborative care model to navigate patients’ desire to avoid a new team while increasing access to specialty palliative care expertise.
Conclusion
A collaborative palliative care model may be welcomed by patients, caregivers, and clinicians in rural areas.
Journal Article