Does GARP really fail miserably? A response to Stockman et al. (2006)

Stockman et al. (2006 ) found that ecological niche models built using DesktopGARP ‘failed miserably’ to predict trapdoor spider (genus Promyrmekiaphila) distributions in California. This apparent failure of GARP (Genetic Algorithm for Rule‐Set Production) was actually a failure of the authors’ methods, that is, attempting to build ecological niche models using single data points. In this paper, we present a re‐analysis of their original data using standard methods with the data appropriately partitioned into training/testing subsets. This re‐evaluation generated accurate distributional predictions that we contrast with theirs. We address the consequences of model‐building using single data points and the need for a foundational understanding of the principles of ecological niche modelling.     

用GARP生态位模型预测刺萼龙葵在中国的潜在分布区

检疫性杂草刺萼龙葵(Solanum rostratum)近年来扩散蔓延到中国华北地区,利用刺萼龙葵在原产地和其他入侵地的分布和14个环境变量,运用GARP生态位模型结合地理信息系统(GIS)对刺萼龙葵在中国的潜在分布区进行了预测,对环境图层的刀切法结果表明, 7个环境变量能提高预测的准确率,适合性卡平方一尾测验表明所建立的模型具有显著的统计学意义,预留数据的受测者工作曲线(ROC)检测表现出很好的预测能力,中国所有已知分布均被正确预测。刺萼龙葵在中国的潜在分布区极广,可以分布在除西藏、青海、海南及两广南部外的其他地区,尤其在华中、华北及华东地区的适生的可能性最高,由此刺萼龙葵可能进入一个危险的快速扩散阶段,应当引起相关部门的重视。     

预测物种潜在分布区——比较SVM与GARP

 物种分布与环境因子之间存在着紧密的联系,因此利用环境因子作为预测物种分布模型的变量是当前最普遍的建模思路,但是绝大多数物种分 布预测模型都遇到了难以解决的“高维小样本\"问题。该研究通过理论和实践证明,基于结构风险最小化原理的支持向量机(Support vector machine, SVM)算法非常适合“高维小样本\"的分类问题。以20种杜鹃花属(Rhododendron)中国特有种为检验对象,利用标本数据和11个1 km×1 km的栅格环境数据层作为模型变量,预测其在中国的潜在分布区,并通过全面的模型评估——专家评估,受试者工作特征(Receiver operator characteristic, ROC)曲线和曲线下方面积(Area under the curve, AUC)——来比较模型的性能。我们实现了以SVM为核心的物种分布预测 系统,并且通过试验证明其无论在计算速度还是预测效果上都远远优于当前广泛使用的规则集合预测的遗传算法(Algorithm for rule-set prediction, GARP)预测系统。     

紫茎泽兰Eupatorium adenophorum Spreng.在中国入侵分布预测

原产于墨西哥的紫茎泽兰Eupatorium adenophorum Spreng.作为一个有害的外来物种在印度、新西兰和澳大利亚生长已有很长时间。在中国,尤其是在南方和西南地区其蔓延速度之快,带来了不可忽视的经济和社会后果。我们采用了生态位模拟新方法来预测紫茎泽兰可能入侵的范围。据此,预测的潜在分布区包括该植物在中国境内已分布的省份及未来华中、华东易受入侵的区域。     

海南岛霸王岭热带天然林景观中主要木本植物关键种的潜在分布

在较大的空间尺度上生态位模型是预测物种潜在分布的有效途径之一。为了探讨在热带天然林景观中木本植物(限于乔木和灌木)主要关键种的潜在分布,在对海南岛霸王岭的热带天然林进行按公里网格样方调查的基础上,采用演替地位和最大潜在高度两个功能性指标对物种进行了功能群划分,并在功能群框架下运用优势度指数法进行了关键种的确定;采用基于地理信息系统(Geographic information system, GIS)的基于规则集合预测的遗传算法(Algorithm for rule-set prediction, GARP)生态位模型对主要关键种的地理分布进行了预测,并应用受试者工作特征分析进行了模型精度验证;应用多元线性回归分析对影响各关键种潜在分布的关键因子进行了确定。结果表明:除了顶极次林层乔木功能群和顶极主林层乔木功能群外,在先锋种功能群、顶极灌木种功能群和顶极超冠层乔木功能群中采用优势度指数法划分出的关键种较为理想;一般来讲,在进行预测的8个关键种中,除了先锋主林层乔木种海南杨桐(Adinandra hainanensis),其它3个先锋种毛稔(Melastoma sanquiueum)、银柴(Aporosa chinensis)和枫香(Liquidambar formosana) 在研究区北部、西部以及西南部均具有较高的发生概率,而顶极种除了顶极超冠层乔木种南亚松(Pinus merkusii)外,九节(Psychotria rubra)、高脚罗伞(Ardisia quinquegona)和海南椎(Castanopsis hainanensis)具有相似的潜在分布格局,在研究区中部、东南部和南部地区具有较高的发生概率;相关分析表明极端最低温、年均温、极端最高温、年均降水量、海拔和坡向6大因子是影响研究区关键种潜在分布的关键因子;精度检验表明,GARP模型对8个关键种的潜在分布预测效果均较好,而其中又以银柴和海南椎的预测精度最高。     

基于GARP 的加拿大一枝黄花在中国的分布区预测

加拿大一枝黄花( Solidago canadensis) 原产北美, 是在中国大陆危害最严重的入侵植物之一。本研究基于大量已有分布点数据, 使用生态位模型(GARP) 对其在中国的潜在扩散区域进行了预测, 结果表明: 极端低温、年均温对加拿大一枝黄花的分布限制较小, 而坡度、坡向、年降雨量、雨日频率、汇流累积量、水流方向、极端高温和霜日频率对其分布影响显著。加拿大一枝黄花的潜在入侵区远大于目前的实际分布区, 因此仍会继续在中国扩散; 中国中南部和东北部是加拿大一枝黄花最易形成入侵的地区, 应采取措施防止其入侵。     

Ecological niche modeling as a predictive tool: silver and bighead carps in North America

The silver carp and bighead carp (Cyprinidae), native to eastern Asia, have been introduced into the United States in attempts to improve water quality in aquaculture ponds, reservoirs, and sewage pools. Escaped or released specimens from fish farms have been reported in many states, and both species are already locally established and spreading further. We used the Genetic Algorithm for Rule-set Prediction (GARP) to model the niches of these two carps in their native ranges using hydrologic and general environmental parameters in concert with native distributional data. The results accurately predicted native occurrence data withheld from the modeling process (P < 0.01). We then projected the niche models onto the North American landscape. Native niche range models significantly predicted known occurrence data from North American introductions (P < 0.001). Further, the models suggest that both species have the potential of spreading throughout the eastern U.S. and selected areas of the West Coast.     

Mapping the geographic distribution of <Emphasis Type="Italic">Aglaia bourdillonii</Emphasis> Gamble (Meliaceae), an endemic and threatened plant,using ecological niche modeling

Aglaia bourdillonii is a plant narrowly endemic to the southern portion of the Western Ghats (WG), in peninsular India. To understand its ecological and geographic distribution, we used ecological niche modeling (ENM) based on detailed distributional information recently gathered, in relation to detailed climatic data sets. The ENMs successfully reconstructed key features of the species’ geographic distribution, focusing almost entirely on the southern WG. Much of the species’ distributional potential is already under protection, but our analysis allows identification of key zones for additional protection, all of which are adjacent to existing protected areas. ENM provides a useful tool for understanding the natural history of such rare and endangered species.

Preliminary distributional analysis of US endangered bird species

A first exploration of applications of ecological niche modeling and geographic distributional prediction to endangered species protection is developed. Foci of richness of endangered bird species are identified in coastal California and along the southern fringe of the United States. Species included on the Endangered Species List on the basis of peripheral populations inflate these concentrations considerably. Species without protection in the US National Park System are focused particularly in peninsular Florida. Application of this methodology to additional taxa and regions holds promise for diverse conservation applications.     

八肋游仆虫一种富含三核苷酸重复序列的新基因GARP的克隆与序列分析

人类基因中三核苷酸重复序列拷贝数的异常扩增, 可导致多种神经系统疾病。一种富含GAA三核苷酸的GARP (glutamic acid-rich protein)基因从八肋游仆虫(Euplotes octocarinatus)大核文库中筛选获得。大核中该基因的染色体全长460 bp, 基因两端具有下毛类纤毛虫大核特有的端粒序列(C₄A₄C₄A₄C₄A₄C₄), 开放读框内含有一个TGA_(88-99)密码子, 在游仆虫中编码为半胱氨酸。经DNA Star 软件分析, 该基因编码的蛋白质由112个氨基酸组成, 预测其分子量为13 kDa, 等电点为3.82, 含有四个 [[alpha]] 螺旋和一个 [[beta]] 折叠。小核中对应的该基因含有两个内部删除序列, IES1 和IES2。IES1和IES2分别长41 bp, IES1以GA二核苷酸直接重复为删除信号, IES2以TA二核苷酸直接重复为删除信号。RT- PCR 证明该基因具有转录活性。