Quantitative Analysis of Fish Morphology Through Landmark and Outline-based Geometric Morphometrics with Free Software.

IF 1 Q3 BIOLOGY Bio-protocol Pub Date : 2024-10-20 DOI:10.21769/BioProtoc.5087
Du Luo
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引用次数: 0

Abstract

Morphology underpins key biological and evolutionary processes that remain elusive. This is in part due to the limitations in robustly and quantitatively analyzing shapes within and between groups in an unbiased and high-throughput manner. Geometric morphometrics (GM) has emerged as a widely employed technique for studying shape variation in biology and evolution. This study presents a comprehensive workflow for conducting geometric morphometric analysis of fish morphology. The step-by-step manual provides detailed instructions for using popular free software, such as the TPS series, MorphoJ, ImageJ, and R, to carry out generalized Procrustes analysis (GPA), principal component analysis (PCA), discriminant function analysis (DFA), canonical variate analysis (CVA), mean shape analysis, and thin plate spline analysis (TPS). The Momocs package in R is specifically utilized for in-depth analysis of fish outlines. In addition, selected functions from the dplyr package are used to assist in the analysis. The full process of fish outline analysis is covered, including extracting outline coordinates, converting and scaling data, defining landmarks, creating data objects, analyzing outline differences, and visualizing results. In conclusion, the current protocol compiles a detailed method for evaluating fish shape variation based on landmarks and outlines. As the field of GM continues to evolve and related software develops rapidly, the limitations associated with morphological analysis of fish are expected to decrease. Interoperable data formats and analytical methods may facilitate the sharing of morphological data and help resolve related scientific problems. The convenience of this protocol allows for fast and effective morphological analysis. Furthermore, this detailed protocol could be adapted to assess image-based differences across a broader range of species or to analyze morphological data of the same species from different origins. Key features • This protocol provides a comprehensive set of commonly used GM-analyzing methods and visualizing skills plus supporting information to help assess the appropriate analysis method • By incorporating both landmarks and outlines, this protocol facilitates a thorough analysis of two-dimensional shape variation in fish, covering a wide range of morphological features • The simplified workflow and detailed procedures make it accessible for non-experienced users to successfully complete the analysis while also providing valuable insights for experienced users Graphical overview Workflow for conducting geometric morphometrics analysis on fish. The steps include image acquisition as data sources, digitization of fish morphology using landmark-based methods, analysis of shape variation characteristics, and visualization of the results in relation to biological interpretation. Largemouth bass (Micropterus salmoides) is used as an example in the schematic representation.

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利用免费软件,通过基于地标和轮廓的几何形态计量学对鱼类形态进行定量分析。
形态学是关键的生物和进化过程的基础,但这些过程仍然难以捉摸。这部分是由于以无偏见和高通量的方式对群体内部和群体之间的形状进行稳健和定量分析的局限性。几何形态计量学(GM)已成为研究生物学和进化中形状变异的一种广泛使用的技术。本研究介绍了对鱼类形态进行几何形态计量分析的综合工作流程。分步操作手册详细说明了如何使用 TPS 系列、MorphoJ、ImageJ 和 R 等常用免费软件进行广义普氏分析(GPA)、主成分分析(PCA)、判别函数分析(DFA)、典型变量分析(CVA)、平均形状分析和薄板样条分析(TPS)。R 软件包 Momocs 专门用于对鱼类轮廓进行深入分析。此外,还使用了 dplyr 软件包中的部分函数来辅助分析。鱼类轮廓分析的整个过程包括提取轮廓坐标、转换和缩放数据、定义地标、创建数据对象、分析轮廓差异以及可视化结果。总之,目前的规程汇编了基于地标和轮廓评估鱼类形状变化的详细方法。随着全球基因组学领域的不断发展和相关软件的快速开发,与鱼类形态分析相关的限制有望减少。可互操作的数据格式和分析方法可促进形态数据的共享,有助于解决相关的科学问题。本方案的便利性使形态分析快速有效。此外,这一详细规程还可用于评估更多物种的图像差异,或分析来自不同产地的同一物种的形态学数据。主要特点 - 本规程提供了一套全面的常用转基因分析方法和可视化技巧,以及辅助信息,以帮助评估适当的分析方法 - 通过结合地标和轮廓,本规程有助于全面分析鱼类的二维形状变化,涵盖了广泛的形态特征 - 简化的工作流程和详细的操作步骤使没有经验的用户也能成功完成分析,同时也为有经验的用户提供了宝贵的见解 图形概述 对鱼类进行几何形态计量学分析的工作流程。步骤包括获取图像作为数据源、使用基于地标的方法对鱼类形态进行数字化、分析形状变化特征以及将结果可视化并与生物学解释联系起来。示意图以大嘴鲈鱼(Micropterus salmoides)为例。
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