<scp>genotypeR</scp>: An integrated <scp>r</scp> package for single nucleotide polymorphism genotype marker design and data analysis

Sefick, Stephen A.; Castronova, Magdalena A.; Stevison, Laurie S.

doi:10.1111/2041-210x.12965

Cited by 4 publications

(3 citation statements)

References 25 publications

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“…As part of a preliminary characterization of plasticity in D. pseudoobscura, Sequenom SNP genotyping markers were designed to genotype crosses between FS14 and FS16 wild-type flies (methods previously described in Stevison et al 2017;Sefick et al 2018). Previously described results captured chromosome 2.…”

Section: Sequenom Snp Genotypingmentioning

confidence: 99%

Putative condition-dependent viability selection in wild type stocks ofDrosophila pseudoobscura

Altindag

Shoben

Stevison

2020

Preprint

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9Meiotic recombination rates vary in response to environmental factors like temperature. 10 Variation in recombination generates an additional source for genetic variation while errors in 11 this pathway can lead to cancer and chromosome number anomalies. Estimating duration and 12 sensitivity of a meiotic response to environmental perturbation requires an understanding of 13 molecular events and well-designed experimental approaches. An earlier study suggested that the 14 peak (most sensitive) timing of plasticity in Drosophila melanogaster occurred during the pre-15 meiotic interphase where DNA replication takes place in S-phase. Recently, heat stress has been 16shown to lead to plasticity in recombination rates in D. pseudoobscura. Here, a combination of 17 molecular genotyping and a series of mutant screens were used to determine peak plasticity 18 timing in this species. Mutant flies were reared in either control or stress temperatures in a 19 traditional cross design. Using mixed model analysis, the odds of crossover formation was 1.53X 20 higher during days 7-9 (p<0.0017) and 1.41X higher on day 9 (p<0.022) in high temperature as 21 compared to control crosses, suggesting the time period as the timing of peak plasticity. Time of 22 peak plasticity at day 9 in D. pseudoobscura can be explained by comparison to the model 23 organism D. melanogaster due to similar timing of key meiotic events. This comparative 24 approach will enable future mechanistic work on the effects of temperature stress on 25 recombination rate. 26

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Section: Sequenom Snp Genotypingmentioning

confidence: 99%

Putative condition-dependent viability selection in wild type stocks ofDrosophila pseudoobscura

Altindag

Shoben

Stevison

2020

Preprint

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“…Here, we have designed single nucleotide polymorphism (SNP) markers for the Sequenom platform [ 114 ], which allows multiplexing of 30–40 markers [ 43 ]. This allowed us to space markers evenly along a single chromosome, providing much more fine-scale plasticity results.…”

Section: Guidelines For Studying Recombination Rate Plasticity To Uncmentioning

confidence: 99%

Recombination rate plasticity: revealing mechanisms by design

Stevison

Sefick

Rushton

et al. 2017

Phil. Trans. R. Soc. B

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For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura.This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

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“…To account for the evenings and mornings being shorter than the nights and days, the same test was repeated but with activity duration normalized by the accumulated available time within the same time windows. Sunset and sunrise defined the time of day; evening was defined as 1 h before and 1 h after sunset, morning as 1 h before and 1 h after the sunrise, day as the period between morning and evening, and night as the period between evening and morning [38]. Differences in activity between the different times of day were tested using Friedman tests.…”

Section: Data Interpretationmentioning

confidence: 99%

Movement and Activity Patterns of Non-Native Wels Catfish (Silurus glanis Linnaeus, 1758) at the Confluence of a Large River and Its Colder Tributary

Nyqvist

Calles

Forneris

et al. 2022

Fishes

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The establishment and proliferation of non-native fish species can have a range of effects within the local ecosystem, including alteration of food webs, nutrient cycling, pathogen dynamics and predation, sometimes also resulting in changed behavior and distribution of native fish species. Knowledge about movements and activity patterns is important to understand the dynamics of non-native animals in their new environment. The Wels catfish (Silurus glanis Linnaeus, 1758) is considered an invasive species in many places in Western Europe, and regional control programs are in place. Here, using radiotelemetry, we study the movements and activity patterns of invasive Wels catfish at an invasion front within the Po River (Italy); namely, at the confluence between the main river, where the species is abundant, and a colder tributary, the Dora Baltea River, where it is absent. In addition, we also investigate potential spatiotemporal overlap between Wels catfish and native and endangered marble trout (Salmo marmoratus Cuvier, 1829) in the area. A total of nine Wels catfish and eight marble trout were tagged. The Wels catfish showed a very high degree of residency within the study area in the Po River, close to the mouth the colder tributary. Despite this, only one catfish entered the lower reaches of the tributary and did so only occasionally during August. No catfish moved further upstream in the tributary. It is likely that lower temperatures in combination with more challenging hydrodynamic conditions made the tributary unattractive to the catfish. The catfish were active during all times of the day but substantially more so during evenings and at nights. Some, but not all, tagged catfish moved to areas in the main stem upstream of the confluence with the tributary. A large proportion of the tagged marble trout made occasional or longer visits to the Po River, with several individuals becoming resident, but without apparent mortality, in the tagged catfish home range. The high residency of the Wels catfish suggests that removal efforts may do well to initially focus on areas close to the habitats of species under conservation concern.

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genotypeR: An integrated r package for single nucleotide polymorphism genotype marker design and data analysis

Cited by 4 publications

References 25 publications

Putative condition-dependent viability selection in wild type stocks ofDrosophila pseudoobscura

Putative condition-dependent viability selection in wild type stocks ofDrosophila pseudoobscura

Recombination rate plasticity: revealing mechanisms by design

Movement and Activity Patterns of Non-Native Wels Catfish (Silurus glanis Linnaeus, 1758) at the Confluence of a Large River and Its Colder Tributary

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