Derryberry Elizabeth P, Derryberry Graham E, Maley James M, Brumfield Robb T
Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Mol Ecol Resour. 2014 May;14(3):652-63. doi: 10.1111/1755-0998.12209. Epub 2013 Dec 27.
We present a new software package (HZAR) that provides functions for fitting molecular genetic and morphological data from hybrid zones to classic equilibrium cline models using the Metropolis-Hastings Markov chain Monte Carlo (MCMC) algorithm. The software applies likelihood functions appropriate for different types of data, including diploid and haploid genetic markers and quantitative morphological traits. The modular design allows flexibility in fitting cline models of varying complexity. To facilitate hypothesis testing, an autofit function is included that allows automated model selection from a set of nested cline models. Cline parameter values, such as cline centre and cline width, are estimated and may be compared statistically across clines. The package is written in the R language and is available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/). Here, we describe HZAR and demonstrate its use with a sample data set from a well-studied hybrid zone in western Panama between white-collared (Manacus candei) and golden-collared manakins (M. vitellinus). Comparisons of our results with previously published results for this hybrid zone validate the hzar software. We extend analysis of this hybrid zone by fitting additional models to molecular data where appropriate.
我们展示了一个新的软件包（HZAR），它提供了一些功能，可使用Metropolis-Hastings马尔可夫链蒙特卡罗（MCMC）算法，将来自杂交带的分子遗传学和形态学数据拟合到经典的平衡渐变群模型。该软件应用适用于不同类型数据的似然函数，包括二倍体和单倍体遗传标记以及定量形态特征。模块化设计使得在拟合不同复杂程度的渐变群模型时具有灵活性。为便于进行假设检验，包含了一个自动拟合函数，可从一组嵌套的渐变群模型中自动选择模型。渐变群参数值，如渐变群中心和渐变群宽度，会被估计出来，并且可以在不同渐变群之间进行统计比较。该软件包用R语言编写，可通过综合R存档网络（CRAN；http://cran.r-project.org/）获取。在此，我们描述HZAR，并通过来自巴拿马西部一个研究充分的白领侏儒鸟（Manacus candei）和金领侏儒鸟（M. vitellinus）杂交带的样本数据集展示其用法。将我们的结果与此前针对该杂交带发表的结果进行比较，验证了hzar软件。我们通过在适当情况下对分子数据拟合额外的模型，扩展了对这个杂交带的分析。
