Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York, USA.
Biology PhD Program, CUNY Graduate Center, New York, New York, USA.
Mol Ecol. 2023 May;32(9):2144-2150. doi: 10.1111/mec.16872. Epub 2023 Feb 12.
The genomics revolution continues to change how ecologists and evolutionary biologists study the evolution and maintenance of biodiversity. It is now easier than ever to generate large molecular data sets consisting of hundreds to thousands of independently evolving nuclear loci to estimate a suite of evolutionary and demographic parameters. However, any inferences will be incomplete or inaccurate if incorrect taxonomic identities and perpetuated throughout the analytical pipeline. Due to decades of research and comprehensive online databases, sequencing and analysis of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and select nuclear genes can provide researchers with a cost effective and simple means to verify the species identity of samples prior to subsequent phylogeographic and population genomic analysis. The addition of these sequences to genomic studies can also shed light on other important evolutionary questions such as explanations for gene tree-species tree discordance, species limits, sex-biased dispersal patterns, adaptation, and mtDNA introgression. Although the mtDNA and cpDNA genomes often should not be used exclusively to make historical inferences given their well-known limitations, the addition of these data to modern genomic studies adds little cost and effort while simultaneously providing a wealth of useful data that can have significant implications for both basic and applied research.
基因组学革命继续改变着生态学家和进化生物学家研究生物多样性的进化和维持方式。现在，比以往任何时候都更容易生成由数百到数千个独立进化的核基因座组成的大型分子数据集，以估计一系列进化和人口统计学参数。然而，如果不正确的分类学身份在分析管道中持续存在，任何推断都将是不完整或不准确的。由于数十年来的研究和全面的在线数据库，对线粒体 DNA（mtDNA）、叶绿体 DNA（cpDNA）和精选核基因的测序和分析可以为研究人员提供一种经济有效的简单方法，在随后的系统地理学和种群基因组分析之前，验证样本的物种身份。将这些序列添加到基因组研究中也可以揭示其他重要的进化问题，例如基因树-物种树分歧、物种界限、性别偏向的扩散模式、适应和 mtDNA 渐渗的解释。尽管由于其众所周知的局限性，mtDNA 和 cpDNA 基因组通常不应单独用于进行历史推断，但将这些数据添加到现代基因组研究中几乎不会增加成本和工作量，同时提供大量有用的数据，这些数据对基础研究和应用研究都具有重要意义。
