📚 Molecular Comparisons Between Species | 物种分子比较
By analysing biological molecules – DNA, RNA and proteins – scientists can quantify the evolutionary relationships between organisms. These molecular techniques provide objective and measurable data that often complement or refine traditional classification based on anatomy and fossils. This article explores the key methods used for molecular comparisons, their underlying principles, and the insights they offer into the tree of life.
通过分析生物大分子——DNA、RNA 和蛋白质，科学家能够定量评估不同物种之间的进化关系。这些分子技术提供了客观且可测量的数据，往往可以补充或修正基于解剖学和化石的传统分类。本文将探讨分子比较的主要方法、其基本原理，以及它们对生命之树提供的深刻洞察。
1. The Basis of Molecular Comparisons | 分子比较的基础
The central idea is that the more recently two species diverged from a common ancestor, the more similar their DNA and protein sequences will be. Mutations accumulate over time at relatively steady rates for certain genes or proteins, turning these molecules into ‘molecular clocks’ that record evolutionary history.
核心思想是：两个物种从共同祖先分歧的时间越近，它们的 DNA 和蛋白质序列就越相似。对于某些基因或蛋白质，突变会以相对稳定的速率随时间累积，从而使这些分子成为记录进化历史的“分子钟”。
2. DNA-DNA Hybridisation | DNA-DNA 杂交
This technique measures overall similarity between the DNA of two species. The double-stranded DNA from each species is extracted, heated to separate the strands, and then mixed so that hybrid double helices form between complementary sequences from the two species. The temperature at which these hybrid molecules separate (melt) indicates the degree of base pairing: a higher melting temperature means more hydrogen bonds, hence greater sequence similarity.
该技术用于衡量两个物种 DNA 之间的整体相似度。分别提取两个物种的双链 DNA，加热解旋成单链，然后混合，让来自不同物种的互补序列形成杂交双螺旋。这些杂交分子分离（解链）的温度反映了碱基配对的匹配程度：解链温度越高，说明氢键越多，序列相似性越高。
3. Direct DNA Sequencing and Sequence Alignment | 直接 DNA 测序与序列比对
Modern Sanger and next-generation sequencing technologies allow scientists to determine the exact nucleotide order of specific genes or whole genomes. Once sequences are obtained, they are aligned using software to identify similarities and differences. By counting the number of base substitutions, insertions or deletions between two species, a quantitative measure of genetic distance can be calculated and used to build phylogenetic trees.
现代 Sanger 测序和新一代测序技术使科学家能够测定特定基因乃至整个基因组的确切核苷酸顺序。获得序列后，利用软件进行比对，找出相似与差异。通过计算两个物种之间的碱基替换、插入或缺失数目，可以得出遗传距离的定量指标，并用于构建系统发育树。
4. Mitochondrial DNA (mtDNA) Comparisons | 线粒体 DNA 比较
Mitochondrial DNA is often used for molecular comparisons because it evolves faster than nuclear DNA, has a high copy number, and is inherited only through the maternal line in most animals. Regions such as the cytochrome c oxidase subunit I (COI) gene serve as DNA barcodes for species identification. Comparing mtDNA sequences can reveal recent evolutionary divergences and track maternal lineages.
线粒体 DNA 常用于分子比较，因为它比核 DNA 进化更快、拷贝数高，且在多数动物中仅通过母系遗传。细胞色素 c 氧化酶亚基 I（COI）等基因区域被用作物种鉴定的 DNA 条形码。通过比较 mtDNA 序列，可揭示近期的进化分歧，追踪母系谱系。
5. Ribosomal RNA (rRNA) Gene Comparisons | 核糖体 RNA 基因比较
Genes encoding ribosomal RNA, such as 16S rRNA in prokaryotes and 18S rRNA in eukaryotes, are highly conserved yet contain variable regions that mutate slowly. This makes them ideal for studying deep evolutionary relationships – for instance, distinguishing between the three domains of life (Bacteria, Archaea and Eukarya). The universal presence and functional constancy of rRNA genes provide a reliable molecular chronometer.
编码核糖体 RNA 的基因，如原核生物的 16S rRNA 和真核生物的 18S rRNA，高度保守，但其中含有缓慢突变的可变区域。这使它们成为研究深层进化关系的理想选择——例如，区分生命三域（细菌、古菌和真核生物）。rRNA 基因的普遍存在与功能恒定性提供了一个可靠的分子计时器。
6. Protein Sequence Comparisons: Amino Acid Differences | 蛋白质序列比较：氨基酸差异
Instead of looking at DNA directly, one can compare the amino acid sequences of the same protein from different species. The number of amino acid differences reflects the number of mutations that have been fixed since the species last shared a common ancestor. A classic example is the protein cytochrome c, which shows only a few amino acid substitutions between closely related species and many more between distantly related ones.
除了直接比较 DNA，还可以比较不同物种中同一蛋白质的氨基酸序列。氨基酸差异的数量反映了自物种拥有最后共同祖先以来累积的突变数。典型的例子是细胞色素 c 蛋白，在亲缘关系近的物种之间只有少数几个氨基酸替换，而在亲缘关系远的物种之间则差异巨大。
7. Cytochrome c and Its Role in Phylogeny | 细胞色素 c 及其在系统发育中的作用
Cytochrome c is a small haem protein involved in the electron transport chain. Its amino acid sequence is remarkably conserved across eukaryotes. For instance, human and chimpanzee cytochrome c are identical, whereas human and yeast cytochrome c differ in about 44 amino acid positions. By aligning these sequences, researchers can infer phylogenetic relationships that closely match those obtained from fossil records and morphology.
细胞色素 c 是一种参与电子传递链的小血红素蛋白，其氨基酸序列在真核生物中极其保守。例如，人类和黑猩猩的细胞色素 c 完全相同，而人类和酵母的细胞色素 c 则有约 44 个氨基酸位点的差异。通过比对序列，研究人员可以推断出系统发育关系，这与化石记录和形态学得到的结果高度吻合。
8. Immunological Comparisons: Antigen–Antibody Reactions | 免疫学比较：抗原-抗体反应
Before routine DNA sequencing was possible, scientists compared serum proteins using antibodies. A protein, such as albumin, from one species is injected into a different species (e.g., a rabbit) to raise antibodies. These antibodies are then tested against the same protein from a range of species. The degree of precipitation or agglutination indicates the similarity: more precipitate means the protein is more similar to the original antigen, reflecting closer evolutionary ties.
在 DNA 测序普及之前，科学家利用抗体比较血清蛋白。将某一物种的蛋白质（如白蛋白）注射到另一种动物（如兔子）体内产生抗体，再用这些抗体与一系列物种的同一蛋白质进行测试。沉淀或凝集的程度反映了相似性：沉淀越多，说明该蛋白质与原始抗原越相似，进化关系越近。
9. The Molecular Clock Hypothesis | 分子钟假说
Many molecular comparisons assume a molecular clock, meaning that for a given gene or protein, mutations occur at a roughly constant rate over evolutionary time. By calibrating this rate with fossil records or known divergence dates, the number of molecular differences between two species can be converted into an estimate of the time since they split. While not perfectly regular, the clock concept works well for many conserved molecules.
许多分子比较都基于分子钟假说，即特定基因或蛋白质在进化过程中突变速率大致恒定。通过化石记录或已知分化时间进行校准，就可以将两个物种之间的分子差异数转化为它们自分歧以来的时间估算值。尽管并非绝对规整，分子钟概念对许多保守分子仍是有效的工具。
10. Bioinformatics and the Construction of Phylogenetic Trees | 生物信息学与系统发育树的构建
Raw sequence data are analysed using bioinformatics tools. Alignment algorithms and software like BLAST, Clustal Omega, or MEGA help identify homologous sequences and construct phylogenetic trees using methods such as maximum parsimony, maximum likelihood or Bayesian inference. These trees visually represent evolutionary relationships, with branch lengths often reflecting genetic distance.
原始序列数据通过生物信息学工具进行分析。比对算法以及 BLAST、Clustal Omega 或 MEGA 等软件有助于识别同源序列，并使用最大简约法、最大似然法或贝叶斯推断等方法构建系统发育树。这些树形图直观地展现进化关系，分支长度通常反映遗传距离。
11. Advantages of Molecular Over Morphological Comparisons | 分子比较相对于形态比较的优势
Molecular comparisons can resolve relationships where morphology is ambiguous – for example, in species that have undergone convergent evolution or dramatic adaptive changes. Molecules are not affected by environmental influences during development, they provide vast amounts of quantitative data, and they allow comparisons across very distantly related organisms, such as bacteria and mammals, which share few morphological features.
分子比较可以解决形态比较模棱两可的问题——例如，对于经历了趋同进化或巨大适应性变化的物种。分子不受发育过程中环境因素的影响，能提供海量定量数据，且允许对亲缘关系极远的生物进行比较，比如细菌和哺乳动物，它们几乎没有共同的形态特征。
12. Limitations and Considerations | 局限性及注意事项
Molecular methods are not without limitations. Horizontal gene transfer, especially in prokaryotes, can confuse phylogenetic signals. Different genes can evolve at different rates, and strict molecular clocks may not apply to all lineages. Furthermore, ancient DNA degradation and incomplete lineage sorting can obscure true evolutionary history. Therefore, molecular evidence is best interpreted alongside morphological, embryological and fossil data.
分子方法也存在局限。基因水平转移（尤其在原核生物中）可能混淆系统发育信号。不同基因的进化速率不同，严格的分子钟未必适用于所有谱系。此外，古 DNA 降解和不完全谱系分选会模糊真实的进化历史。因此，分子证据最好结合形态学、胚胎学和化石数据共同解读。
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