Adult Females with Barium (Ba) and Strontium (Sr) Data

Research article: Epigenetic response of Louisiana Waterthrush (Parkesia motacilla) related to shale gas development

Journal: Ibis

Citation: M. W. Frantz, P. B. Wood, S. Latta, and A. Welsh. 2019. Epigenetic response of Louisiana Waterthrush (Parkesia motacilla) related to shale gas development. Ibis In Review.

Contact information: Mack W. Frantz; [e-mail]; West Virginia Cooperative Fish and Wildlife Research Unit, Davis College, School of Natural Resources, West Virginia University, P.O. Box 6125, Morgantown, WV, USA

Analysis description: If TerrGas or TerrRunoff was statistically significant for adult females, the restriction sites driving the overall differential methylation were used to correlate the total amount of methylation across restriction sites to Barium (Ba) and Stontium (Sr) heavy concentrations bioaccumulated in waterthrush feathers. Otherwise, all restriction sites were used. The test was limited to waterthrush sampled in 2013 that had both blood samples and Ba and Sr feather data from Latta et al. (2015). A Box-Cox transformation was performed on Ba and Sr data (in ppm) to approach normality using R package car (Fox et al. 2015). We used the transformed Ba and Sr data to conduct a Pearson correlation of the total amount of methylation across restriction sites to Ba and Sr concentrations using R package psych (Revelle 2017) in R (R Core Team 2014).
See research article for additional information regarding methdology, terms, and data significance.

Data description: Adult females with Strontium (Sr) and Barium (Ba) data from 2013 have Box-Cox transformed ppm values displayed as used in the Pearson correlations.
Columns A and B have heavy metal values used in analysis. Column C indicates the number of methylated restriction sites across all restriction sites (n=100).
Four adult female recaptures had Ba and Sr data described.

Research article relationship: Data referenced in Table 3 and displayed in Fig. 1.

References:
Fox, J., Weisberg, S., Adler, D., Bates, D., Baud-Bovy, G., Ellison, S., Firth, D., Friendly, M., Gorjanc, G., Graves, S., Heiberger, R., Laboissiere, R., Monette, G., Murdoch, D., Nilsson, H., Ogle, D., Ripley, B., Venables, W., Winsemius, D., Zeileis, A., & R-Core. 2017. Package ‘car’. Version 2.1-5. https://CRAN.R-project.org/package=car (accessed 2017 July 19).

Latta, S.C., Marshall, L.C., Frantz, M.W., & Toms, J. 2015. Evidence from two shale regions that a riparian songbird accumulates metals associated with hydraulic fracturing. Ecosphere 6: 144.

R Development Core Team. 2014. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

Revelle, W. 2017. Package ‘psych’. Version 1.7.5. https://CRAN.Rproject.org/package=psych (accessed 2017 July 19).

研究论文：路易斯安那水鵖（Parkesia motacilla）的表观遗传反应与页岩气开发相关

期刊：Ibis

引用：M. W. Frantz, P. B. Wood, S. Latta, 和 A. Welsh. 2019. 路易斯安那水鵖（Parkesia motacilla）的表观遗传反应与页岩气开发. Ibis In Review.

联系方式：Mack W. Frantz；[e-mail]；西弗吉尼亚大学自然资源学院戴维斯学院，西弗吉尼亚大学合作鱼类和野生动物研究单位，邮政信箱 6125，摩根敦，WV，美国

分析描述：若TerrGas或TerrRunoff对成年雌性具有统计学意义，则使用驱动整体差异甲基化的限制位点来关联限制位点间的总甲基化量与水鵖羽毛中累积的重浓度钡（Ba）和锶（Sr）。否则，使用所有限制位点。测试仅限于2013年采集的既有血液样本又有Ba和Sr羽毛数据的路易斯安那水鵖（参见Latta等，2015年）。使用R包car（Fox等，2015年）对Ba和Sr数据（以ppm计）进行了Box-Cox转换，以接近正态性。我们使用转换后的Ba和Sr数据，在R（R Core Team，2014年）中利用R包psych（Revelle，2017年）进行Pearson相关分析，将限制位点间的总甲基化量与Ba和Sr浓度关联。

参见研究论文以获取关于方法、术语和数据重要性的更多信息。

数据描述：2013年成年雌性具有锶（Sr）和钡（Ba）数据，Box-Cox转换后的ppm值用于Pearson相关分析。
列A和B包含分析中使用的重金属值。列C表示所有限制位点中的甲基化限制位点数量（n=100）。有四只成年雌性重捕的水鵖描述了Ba和Sr数据。

研究论文关系：数据参考表3并在图1中展示。

参考文献：
Fox, J., Weisberg, S., Adler, D., Bates, D., Baud-Bovy, G., Ellison, S., Firth, D., Friendly, M., Gorjanc, G., Graves, S., Heiberger, R., Laboissiere, R., Monette, G., Murdoch, D., Nilsson, H., Ogle, D., Ripley, B., Venables, W., Winsemius, D., Zeileis, A., & R-Core. 2017. 软件包‘car’。版本2.1-5. https://CRAN.R-project.org/package=car（访问日期：2017年7月19日）。
Latta, S.C., Marshall, L.C., Frantz, M.W., & Toms, J. 2015. 来自两个页岩区的证据表明，河岸鸣禽积累与水力压裂相关的金属。Ecosphere 6: 144。
R Development Core Team. 2014. R：一种用于统计计算的编程语言和环境。奥地利维也纳，R基金会。
Revelle, W. 2017. 软件包‘psych’。版本1.7.5。https://CRAN.R-project.org/package=psych（访问日期：2017年7月19日）。