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Article ; Online: CKMRpop: Forward-in-time simulation and tabulation of pairwise kin relationships in age-structured populations.

Anderson, Eric C

2021 Volume 22, Issue 3, Page(s) 1190–1199

Abstract: In the last five years, interest in close-kin mark-recapture (CKMR), a variant of mark-recapture that uses genetically inferred kin as 'recaptures', has grown dramatically. However, understanding the basis of CKMR, and properly implementing it, remains ... ...

Abstract	In the last five years, interest in close-kin mark-recapture (CKMR), a variant of mark-recapture that uses genetically inferred kin as 'recaptures', has grown dramatically. However, understanding the basis of CKMR, and properly implementing it, remains challenging. This paper describes an R package, CKMRpop, for simulating age-structured populations with user-specified demography, overdispersed variance in reproductive success (allowing for different ratios of effective to census size) and random sampling of individuals. Using compiled code for the simulation makes it feasible to simulate populations of millions of individuals. From the simulation output, pairs of sampled individuals related within a user-specified number of generations are found. Such pairs form the foundation for CKMR inference, and simulating them provides insight for understanding the statistical basis for CKMR and for assessing the feasibility of CKMR in different scenarios. We predict that CKMRpop will serve as an important tool for researchers contemplating CKMR estimation of population size. Furthermore, the methods presented here for identifying and categorizing relationships beyond half-siblings allow a more complete picture of the wide variety of kin pairs encountered in populations. This identifies the fraction of kin pairs that may not be the target of a CKMR experiment, but may be inadvertently mistaken for a more closely related 'target' kin pair. Additionally, as more distant kin categories will likely be accurately inferred from increasingly available and inexpensive whole genome resequencing, understanding the distributions of more distant relationships in populations is a first step towards broadening the scope of CKMR to include them.
MeSH term(s)	Computer Simulation ; Humans ; Population Density ; Sequence Analysis, DNA
Language	English
Publishing date	2021-10-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13513
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Article: CKMRpop: Forward‐in‐time simulation and tabulation of pairwise kin relationships in age‐structured populations

Anderson, Eric C.

Molecular ecology resources. 2022 Apr., v. 22, no. 3

2022

Abstract: In the last five years, interest in close‐kin mark–recapture (CKMR), a variant of mark–recapture that uses genetically inferred kin as ‘recaptures’, has grown dramatically. However, understanding the basis of CKMR, and properly implementing it, remains ... ...

Abstract	In the last five years, interest in close‐kin mark–recapture (CKMR), a variant of mark–recapture that uses genetically inferred kin as ‘recaptures’, has grown dramatically. However, understanding the basis of CKMR, and properly implementing it, remains challenging. This paper describes an R package, CKMRpop, for simulating age‐structured populations with user‐specified demography, overdispersed variance in reproductive success (allowing for different ratios of effective to census size) and random sampling of individuals. Using compiled code for the simulation makes it feasible to simulate populations of millions of individuals. From the simulation output, pairs of sampled individuals related within a user‐specified number of generations are found. Such pairs form the foundation for CKMR inference, and simulating them provides insight for understanding the statistical basis for CKMR and for assessing the feasibility of CKMR in different scenarios. We predict that CKMRpop will serve as an important tool for researchers contemplating CKMR estimation of population size. Furthermore, the methods presented here for identifying and categorizing relationships beyond half‐siblings allow a more complete picture of the wide variety of kin pairs encountered in populations. This identifies the fraction of kin pairs that may not be the target of a CKMR experiment, but may be inadvertently mistaken for a more closely related ‘target’ kin pair. Additionally, as more distant kin categories will likely be accurately inferred from increasingly available and inexpensive whole genome resequencing, understanding the distributions of more distant relationships in populations is a first step towards broadening the scope of CKMR to include them.
Keywords	demography ; mark-recapture studies ; population size ; reproductive success ; sequence analysis ; variance
Language	English
Dates of publication	2022-04
Size	p. 1190-1199.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13513
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Article: Transcranial direct current stimulation (tDCS) to dorsolateral prefrontal cortex influences perceived pleasantness of food.

Anderson, Eric C / Cantelon, Julie A / Holmes, Amanda / Giles, Grace E / Brunyé, Tad T / Kanarek, Robin

Heliyon

2023 Volume 9, Issue 2, Page(s) e13275

Abstract: The ability to regulate the intake of unhealthy foods is critical in modern, calorie dense food environments. Frontal areas of the brain, such as the dorsolateral prefrontal cortex (DLPFC), are thought to play a central role in cognitive control and ... ...

Abstract	The ability to regulate the intake of unhealthy foods is critical in modern, calorie dense food environments. Frontal areas of the brain, such as the dorsolateral prefrontal cortex (DLPFC), are thought to play a central role in cognitive control and emotional regulation. Therefore, increasing activity in the DLPFC may enhance these functions which could improve the ability to reappraise and resist consuming highly palatable but unhealthy foods. One technique for modifying brain activity is transcranial direct current stimulation (tDCS), a non-invasive technique for modulating neuronal excitability that can influence performance on a range of cognitive tasks. We tested whether anodal tDCS targeting the right DLPFC would influence how people perceived highly palatable foods. In the present study, 98 participants were randomly assigned to receive a single session of active tDCS (2.0 mA) or sham stimulation. While receiving active or sham stimulation, participants viewed images of highly palatable foods and reported how pleasant it would be to eat each food (liking) and how strong their urge was to eat each food (wanting). We found that participants who received active versus sham tDCS stimulation perceived food as less pleasant, but there was no difference in how strong their urge was to eat the foods. Our findings suggest that modulating excitability in the DLPFC influences "liking" but not "wanting" of highly palatable foods. Non-invasive brain stimulation might be a useful technique for influencing the hedonic experience of eating but more work is needed to understand when and how it influences food cravings.
Language	English
Publishing date	2023-02-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e13275
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Article ; Online: Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river.

Rizza, Samuel F / Wilzbach, Margaret A / Kinziger, Andrew P / Anderson, Eric C / Carlos Garza, John

The Journal of heredity

2023 Volume 114, Issue 3, Page(s) 219–230

Abstract: Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as 1 of 10 hybrid classes using 30 "diagnostic" single-nucleotide ... ...

Abstract	Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as 1 of 10 hybrid classes using 30 "diagnostic" single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e. jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.
MeSH term(s)	Animals ; Female ; Male ; Oncorhynchus mykiss/genetics ; Rivers ; Oncorhynchus/genetics ; Hybridization, Genetic ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2023-06-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3044-2
ISSN	1465-7333 ; 0022-1503
ISSN (online)	1465-7333
ISSN	0022-1503
DOI	10.1093/jhered/esad022
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Article: Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead.

Goetz, Laura C / Nuetzel, Hayley / Vendrami, David L J / Beulke, Anne K / Anderson, Eric C / Garza, John Carlos / Pearse, Devon E

Evolutionary applications

2024 Volume 17, Issue 3, Page(s) e13681

Abstract: 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 ... ...

Abstract	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
Language	English
Publishing date	2024-03-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2405496-3
ISSN	1752-4563 ; 1752-4571
ISSN (online)	1752-4563
ISSN	1752-4571
DOI	10.1111/eva.13681
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Article ; Online: Transcranial direct current stimulation (tDCS) to dorsolateral prefrontal cortex influences perceived pleasantness of food

Anderson, Eric C. / Cantelon, Julie A. / Holmes, Amanda / Giles, Grace E. / Brunyé, Tad T. / Kanarek, Robin

Heliyon. 2023 Feb., v. 9, no. 2 p.e13275-

2023

Abstract	The ability to regulate the intake of unhealthy foods is critical in modern, calorie dense food environments. Frontal areas of the brain, such as the dorsolateral prefrontal cortex (DLPFC), are thought to play a central role in cognitive control and emotional regulation. Therefore, increasing activity in the DLPFC may enhance these functions which could improve the ability to reappraise and resist consuming highly palatable but unhealthy foods. One technique for modifying brain activity is transcranial direct current stimulation (tDCS), a non-invasive technique for modulating neuronal excitability that can influence performance on a range of cognitive tasks. We tested whether anodal tDCS targeting the right DLPFC would influence how people perceived highly palatable foods. In the present study, 98 participants were randomly assigned to receive a single session of active tDCS (2.0 mA) or sham stimulation. While receiving active or sham stimulation, participants viewed images of highly palatable foods and reported how pleasant it would be to eat each food (liking) and how strong their urge was to eat each food (wanting). We found that participants who received active versus sham tDCS stimulation perceived food as less pleasant, but there was no difference in how strong their urge was to eat the foods. Our findings suggest that modulating excitability in the DLPFC influences "liking" but not "wanting" of highly palatable foods. Non-invasive brain stimulation might be a useful technique for influencing the hedonic experience of eating but more work is needed to understand when and how it influences food cravings.
Keywords	cognition ; neurons ; people ; prefrontal cortex ; Brain stimulation ; tDCS ; Craving ; Liking ; Wanting
Language	English
Dates of publication	2023-02
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e13275
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Article ; Online: Null effects of therapy dog interaction on adolescent anxiety during a laboratory-based social evaluative stressor.

Mueller, Megan K / Anderson, Eric C / King, Erin K / Urry, Heather L

Anxiety, stress, and coping

2021 Volume 34, Issue 4, Page(s) 365–380

Abstract: Background and objectives: Animal-assisted interventions (AAIs) are increasingly popular as treatments to reduce anxiety. However, there is little empirical evidence testing the mechanisms of action in AAIs, especially among adolescents. We examined ... ...

Abstract	Background and objectives: Animal-assisted interventions (AAIs) are increasingly popular as treatments to reduce anxiety. However, there is little empirical evidence testing the mechanisms of action in AAIs, especially among adolescents. We examined whether two possible mechanisms, social interaction and/or physical contact with a therapy dog, might reduce anxiety during a social stressor. Design and methods: To test these mechanisms, we randomly assigned 75 adolescents with low, middle, and high levels of social anxiety to complete a laboratory-based social evaluative stressor in one of three conditions: social interaction with a therapy dog (no physical interaction), social plus physical interaction with a therapy dog, or no interaction with a therapy dog. We measured self-reported anxiety and autonomic reactivity during the social stressor to assess the effects of contact with a therapy dog. Results and conclusions: We found no evidence that the presence of a real dog, with or without the opportunity to touch it, reduced anxiety or autonomic reactivity or improved cognitive performance relative to the presence of a stuffed dog in the control condition, regardless of levels of preexisting social anxiety.
MeSH term(s)	Adolescent ; Animals ; Anxiety ; Anxiety Disorders ; Dogs ; Fear ; Humans ; Laboratories ; Therapy Animals
Language	English
Publishing date	2021-03-02
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural
ZDB-ID	1115932-7
ISSN	1477-2205 ; 1061-5806
ISSN (online)	1477-2205
ISSN	1061-5806
DOI	10.1080/10615806.2021.1892084
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Article ; Online: Polygenic Basis and the Role of Genome Duplication in Adaptation to Similar Selective Environments.

Campbell, Matthew A / Anderson, Eric C / Garza, John Carlos / Pearse, Devon E

The Journal of heredity

2021 Volume 112, Issue 7, Page(s) 614–625

Abstract: Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants ... ...

Abstract	Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and nonparallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while 3 of the 4 populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these 2 inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.
MeSH term(s)	Adaptation, Physiological/genetics ; Animal Migration ; Animals ; Ecotype ; Gene Duplication ; Genome ; Oncorhynchus mykiss/genetics
Language	English
Publishing date	2021-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3044-2
ISSN	1465-7333 ; 0022-1503
ISSN (online)	1465-7333
ISSN	0022-1503
DOI	10.1093/jhered/esab049
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Article: "Doing Good" in U.S. Cancer Genomics? Valuation practices across the boundaries of research and care in rural community oncology.

Darling, Katherine Weatherford / Kohut, Michael / Leeds, Susan / Anderson, Eric C / Han, Paul K J

New genetics and society

2022 Volume 41, Issue 3, Page(s) 254–283

Abstract: Genomic Tumour Testing (GTT) is an emerging site of "experimental care" in oncology [Cambrosio, Alberto, Peter Keating, Etienne Vignola-Gagné, Sylvain Besle, and Pascale Bourret. 2018a. "Extending Experimentation: Oncology's Fading Boundary Bbetween ... ...

Abstract	Genomic Tumour Testing (GTT) is an emerging site of "experimental care" in oncology [Cambrosio, Alberto, Peter Keating, Etienne Vignola-Gagné, Sylvain Besle, and Pascale Bourret. 2018a. "Extending Experimentation: Oncology's Fading Boundary Bbetween Research and Care."
Language	English
Publishing date	2022-07-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1483823-0
ISSN	1463-6778
ISSN	1463-6778
DOI	10.1080/14636778.2022.2091532
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Article ; Online: Purging putative siblings from population genetic data sets: a cautionary view.

Waples, Robin S / Anderson, Eric C

Molecular ecology

2017 Volume 26, Issue 5, Page(s) 1211–1224

Abstract: Interest has surged recently in removing siblings from population genetic data sets before conducting downstream analyses. However, even if the pedigree is inferred correctly, this has the potential to do more harm than good. We used computer simulations ...

Abstract	Interest has surged recently in removing siblings from population genetic data sets before conducting downstream analyses. However, even if the pedigree is inferred correctly, this has the potential to do more harm than good. We used computer simulations and empirical samples of coho salmon to evaluate strategies for adjusting samples to account for family structure. We compared performance in full samples and sibling-reduced samples of estimators of allele frequency (P^), population differentiation (F^ST) and effective population size (N^e). Results: (i) unless simulated samples included large family groups together with a component of unrelated individuals, removing siblings generally reduced precision of P^ and F^ST; (ii) N^e based on the linkage disequilibrium method was largely unbiased using full random samples but became increasingly upwardly biased under aggressive purging of siblings. Under nonrandom sampling (some families over-represented), N^e using full samples was downwardly biased; removing just the right 'Goldilocks' fraction of siblings could produce an unbiased estimate, but this sweet spot varied widely among scenarios; (iii) weighting individuals based on the inferred pedigree (to produce a best linear unbiased estimator, BLUE) maximized precision of P^ when the inferred pedigree was correct but performed poorly when the pedigree was wrong; (iv) a variant of sibling removal that leaves intact small sibling groups appears to be more robust to errors in inferences about family structure. Our results illustrate the complex challenges posed by presence of family structure, suggest that no single optimal solution exists and argue for caution in adjusting population genetic data sets for the presence of putative siblings without fully understanding the consequences.
Language	English
Publishing date	2017-03
Publishing country	England
Document type	News
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.14022
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