Molecular Comparisons Between Species and Evolutionary Relationships | 物种间分子比较与亲缘关系

📚 Molecular Comparisons Between Species and Evolutionary Relationships | 物种间分子比较与亲缘关系

Molecular comparisons between species provide one of the most powerful and reliable ways to determine evolutionary relationships. By analysing DNA sequences, protein structures and immunological responses, biologists can construct accurate phylogenetic trees that reveal how closely related different organisms are.

物种间的分子比较是推断亲缘关系最强大、最可靠的方法之一。通过分析DNA序列、蛋白质结构和免疫学反应，生物学家可以构建准确的系统发育树，揭示不同生物之间的亲缘关系远近。

1. Why Molecular Comparisons? | 为什么选择分子比较？

Traditional taxonomy relied on morphological features such as bone structure, flower shape or body symmetry. However, morphological similarity can arise from convergent evolution rather than common ancestry, leading to incorrect classifications.

传统的分类学依赖于形态学特征，如骨骼结构、花形或身体对称性。然而，形态上的相似可能源于趋同进化而非共同祖先，从而导致错误的分类。

Molecular data overcome this limitation by comparing the actual genetic material or protein products that are inherited directly from generation to generation. Genes change slowly over time through mutations, so the number of differences between two species reflects the time since they diverged from a common ancestor.

分子数据通过比较直接代代遗传的遗传物质或蛋白质产物，克服了上述局限。基因通过突变随时间缓慢变化，因此两个物种之间的差异数量反映了它们自共同祖先分化以来所经历的时间。

Key advantages of molecular comparisons include:

They are quantitative and objectively comparable between distantly related groups.
They are less affected by environmental adaptation and convergent evolution.
They can be applied to any organism, including extinct species via ancient DNA.

它们是定量的，可在亲缘关系较远的类群之间进行客观比较。
它们较少受到环境适应和趋同进化的影响。
它们可用于任何生物，包括通过古DNA研究灭绝物种。

2. Comparing DNA Base Sequences | 比较DNA碱基序列

Comparing the order of nucleotide bases in genes such as those coding for cytochrome c, rRNA or haemoglobin is one of the most direct methods. Two species that share more identical bases in a given gene are more closely related. Each base substitution represents a mutation that occurred after the two lineages separated.

比较基因中核苷酸碱基的顺序是最直接的方法之一，常用基因包括细胞色素c、rRNA或血红蛋白的编码基因。两个物种在特定基因上拥有的相同碱基越多，亲缘关系就越近。每一次碱基替换都代表两个谱系分离后发生的一次突变。

For example, human and chimpanzee cytochrome c genes differ in only a few bases, whereas human and yeast cytochrome c genes differ in many more. This difference correlates perfectly with the known evolutionary distance between these organisms.

例如，人类和黑猩猩的细胞色素c基因仅有少数碱基差异，而人类和酵母菌的细胞色素c基因差异则多得多。这种差异与已知的这些生物之间的进化距离完美相关。

DNA hybridisation is a technique that measures the overall similarity of two genomes. When DNA from two species is heated and mixed, complementary strands bind to form hybrid double helices. The higher the temperature required to separate these hybrids, the more complementary the sequences are, and the closer the evolutionary relationship.

DNA杂交是一种衡量两个基因组总体相似度的技术。将来自两个物种的DNA加热并混合，互补链会结合形成杂交双螺旋。解离这些杂交分子所需的温度越高，说明序列互补性越强，亲缘关系就越近。

Hybrid stability ∝ sequence complementarity ∝ evolutionary closeness

杂交稳定性 ∝ 序列互补性 ∝ 进化上的亲近程度

3. Protein Amino Acid Sequence Comparison | 蛋白质氨基酸序列比较

Proteins are the translation products of genes, and their amino acid sequences reflect the DNA sequence they came from. Comparing amino acid sequences is often more practical than comparing DNA directly because proteins are more stable and can be extracted from preserved specimens.

蛋白质是基因翻译的产物，其氨基酸序列反映了编码它们的DNA序列。比较氨基酸序列通常比直接比较DNA更实用，因为蛋白质更稳定，可以从保存的标本中提取。

Cytochrome c is a small protein of about 104 amino acids found in the mitochondria of all aerobic organisms. It is highly conserved because its function in electron transport is essential. However, the small differences that do occur accumulate at a steady rate, making it ideal for studying relationships between distantly related species.

细胞色素c是一种约含104个氨基酸的小型蛋白质，存在于所有需氧生物的线粒体中。由于其在电子传递链中的功能至关重要，该蛋白质高度保守。然而，确实发生的小差异会以恒定速率积累，使其成为研究远缘物种亲缘关系的理想材料。

Haemoglobin is a larger protein with more variable regions, making it suitable for comparing closely related species. The number of amino acid differences between two species can be plotted against evolutionary time to estimate divergence dates.

血红蛋白是更大的蛋白质，含有更多可变区域，适合比较亲缘关系较近的物种。两个物种之间的氨基酸差异数可以对照进化时间作图，从而估算分化时间。

Common proteins used in molecular phylogenetics include:

Protein 蛋白质	Function 功能	Suitability 适用性
Cytochrome c	Electron transport 电子传递	Distant species 远缘物种
Haemoglobin	Oxygen transport 氧气运输	Close species 近缘物种
rRNA	Ribosome structure 核糖体结构	All domains 所有域

4. Immunological Comparisons | 免疫学比较

The immune system of an animal produces antibodies that bind specifically to foreign proteins, called antigens. When a protein from species A is injected into a rabbit, the rabbit produces antibodies against it. These antibodies can then be tested against proteins extracted from other species.

动物的免疫系统会产生抗体，特异性结合称为抗原的外源蛋白质。将物种A的蛋白质注射到家兔体内，家兔会产生针对它的抗体。然后可以用这些抗体测试从其他物种提取的蛋白质。

If the antibody-antigen complex forms a precipitate, the antigen is recognised, indicating that species B has proteins similar to species A. The amount of precipitate formed is proportional to how closely related the two species are. This is the basis of the precipitin test.

如果抗体-抗原复合物形成沉淀，则说明抗原被识别，表明物种B具有与物种A相似的蛋白质。形成的沉淀量正比于两个物种的亲缘关系密切程度。这就是沉淀素反应的基础。

More precipitate → more antibody-antigen binding → closer relationship

沉淀越多 → 抗体-抗原结合越多 → 亲缘关系越近

A classic example involves human serum albumin. Antibodies raised against human albumin produce a strong precipitate with chimp albumin, a weaker one with monkey albumin, and little or no precipitate with fish albumin. These results support the known order of evolutionary relationships among these groups.

一个经典例子使用人血清白蛋白。针对人白蛋白产生的抗体会与黑猩猩白蛋白形成强沉淀，与猴白蛋白形成较弱沉淀，与鱼白蛋白几乎不形成沉淀。这些结果支持了这些类群之间已知的进化关系顺序。

5. Comparing DNA Hybridisation and DNA Barcoding | 比较DNA杂交与DNA条形码

DNA hybridisation can also be performed using labelled single-stranded DNA fragments. A radioactive or fluorescent probe from one species is allowed to pair with DNA from another species, and the thermal stability of the resulting hybrid is measured.

DNA杂交也可以使用标记的单链DNA片段进行。来自一个物种的放射性或荧光探针与来自另一物种的DNA配对，并测量所得杂交分子的热稳定性。

DNA barcoding uses a short, standardised gene segment for species identification. For animals, the mitochondrial gene COI (cytochrome c oxidase subunit I) is commonly used because it evolves quickly enough to distinguish species but slowly enough to remain conserved within a species.

DNA条形码使用一个短的标准基因片段进行物种鉴定。对于动物，通常使用线粒体基因COI（细胞色素c氧化酶亚基I），因为它的进化速度足以区分不同物种，但又足够保守以在同一物种内保持稳定。

Differences between DNA hybridisation and DNA barcoding:

DNA hybridisation compares whole genomes or large stretches of DNA.
DNA barcoding compares one specific gene locus.
DNA hybridisation measures overall sequence similarity.
DNA barcoding identifies species against a reference database.

DNA杂交比较全基因组或大片段的DNA。
DNA条形码只比较一个特定基因位点。
DNA杂交衡量整体序列相似性。
DNA条形码通过参考数据库进行物种鉴定。

6. Mitochondrial DNA and Chloroplast DNA | 线粒体DNA与叶绿体DNA

Mitochondrial DNA (mtDNA) is inherited maternally and does not undergo recombination, making it a valuable tool for studying evolutionary relationships through the maternal line. It also has a faster mutation rate than nuclear DNA, making it especially useful for comparing recently diverged species.

线粒体DNA（mtDNA）是母系遗传的，不发生重组，是研究母系进化谱系的宝贵工具。其突变率也高于核DNA，因此特别适合比较近期分化的物种。

Chloroplast DNA (cpDNA) in plants is similarly inherited, usually maternally, and is used extensively in plant phylogenetics. The rbcL gene, which codes for the large subunit of RuBisCO, is one of the most widely used chloroplast markers.

植物中的叶绿体DNA（cpDNA）也通常是母系遗传的，被广泛用于植物系统发育研究。rbcL基因编码RuBisCO大亚基，是最常用的叶绿体标记之一。

The high copy number of mtDNA and cpDNA per cell makes these molecules easier to extract and analyse from degraded or ancient samples, such as bones, hair or preserved tissues.

每个细胞中mtDNA和cpDNA的高拷贝数使得这些分子更容易从降解或古老的样本（如骨骼、毛发或保存的组织）中提取和分析。

Key comparison between mtDNA and nuclear DNA:

线粒体DNA与核DNA的关键比较：

mtDNA is circular; nuclear DNA is linear.
mtDNA is maternally inherited; nuclear DNA is inherited from both parents.
mtDNA has ~10⁻⁴ mutations per base pair per generation; nuclear DNA has fewer.

mtDNA是环状的；核DNA是线性的。
mtDNA为母系遗传；核DNA来自双亲。
mtDNA每代每碱基对的突变率约为10⁻⁴；核DNA的突变率较低。

7. The Molecular Clock | 分子钟

The molecular clock hypothesis states that the number of differences in a given gene or protein between two species increases at an approximately constant rate over evolutionary time. If the rate of mutation is known, the time since two species diverged can be calculated from the degree of molecular difference.

分子钟假说指出，两个物种之间特定基因或蛋白质的差异数量在进化时间中大约以恒定速率增加。如果已知突变速率，就可以根据分子差异程度计算出两个物种分化的时间。

The mathematical relationship can be expressed as:

这种数学关系可以表示为：

Time since divergence = Number of differences ÷ Mutation rate

分化时间 = 差异数量 ÷ 突变速率

To calibrate a molecular clock, researchers use fossils or geological events of known age. For example, if fossils show that two lineages split 10 million years ago and the gene has accumulated 2% difference, then a 4% difference in another pair indicates a split of 20 million years ago.

为了校准分子钟，研究者使用已知年龄的化石或地质事件。例如，如果化石显示两个谱系在1000万年前分化，并且该基因积累了2%的差异，那么另一对物种4%的差异则表明它们在2000万年前分化。

Limitations of the molecular clock include varying mutation rates between different genes, different species and different generations times. Some mutations are silent, causing no change in amino acid sequence, while others are deleterious and removed by natural selection.

分子钟的局限性包括不同基因、不同物种和不同世代时间之间的突变速率不同。有些突变是无义（沉默）的，不引起氨基酸序列变化，而另一些则是有害的，会被自然选择所淘汰。

8. Constructing Phylogenetic Trees | 构建系统发育树

A phylogenetic tree is a branching diagram that represents the evolutionary relationships between organisms. Each branch point, called a node, represents a common ancestor. The length of the branches can represent either time or the amount of molecular change.

系统发育树是一种表示生物之间进化关系的分支图。每个分支点称为节点，代表一个共同祖先。分支的长度可以表示时间或分子变化量。

When constructing a tree from molecular data, scientists align sequences, count differences and use computational algorithms to find the tree that best fits the data. The principle of maximum parsimony is often used: the simplest explanation, requiring the fewest changes, is preferred.

从分子数据构建系统发育树时，科学家比对序列、统计差异，并使用计算算法寻找最符合数据的树。通常使用最大简约原则：需要最少变化的最简单解释是首选。

Maximum parsimony = minimum total evolutionary changes

最大简约 = 总进化变化最小

Reading a phylogenetic tree requires care. Species that share a recent common ancestor are called sister taxa and are located on adjacent branches. However, the order of species at the tips does not necessarily indicate their degree of relatedness; what matters is the branching pattern.

解读系统发育树需要仔细。共享较近共同祖先的物种被称为姊妹类群，位于相邻的分支上。然而，末端物种的排列顺序不一定表示其亲缘程度；关键在于分支模式。

9. Applications and Limitations | 应用与局限

Molecular comparisons have been used to trace the origins of human migrations, identify pathogens in clinical samples, establish paternity and resolve controversial taxonomic classifications. The three-domain system of classification (Bacteria, Archaea and Eukarya) was established largely through rRNA sequence analysis by Carl Woese in 1977.

分子比较已被用于追踪人类迁徙的起源、鉴定临床样本中的病原体、确定亲子关系以及解决有争议的分类学问题。三域分类系统（细菌域、古菌域和真核生物域）主要是由Carl Woese于1977年通过rRNA序列分析建立的。

Despite their power, molecular methods have limitations:

Different genes may produce conflicting trees due to different evolutionary histories.
Horizontal gene transfer can obscure relationships, especially in prokaryotes.
Mutation rates are not always constant, violating the molecular clock assumption.
Sequencing errors or alignment mistakes can distort the results.

尽管分子方法功能强大，但也有局限性：

不同基因可能因为进化历史不同而产生相互冲突的系统发育树。
水平基因转移会模糊亲缘关系，在原核生物中尤其突出。
突变速率并不总是恒定的，这违反了分子钟假设。
测序误差或比对错误会扭曲结果。

In the CIE A-Level syllabus, it is important to remember that molecular evidence is always used alongside morphological, embryological and fossil evidence to build a complete picture of evolutionary relationships. No single source of evidence is sufficient on its own.

在CIE A-Level考纲中，需要记住的是，分子证据总是与形态学、胚胎学和化石证据一起使用，以构建完整的进化关系图景。单一证据来源往往是不够的。

10. Summary of Key Points for Revision | 考点总结

For exam preparation, focus on the following core ideas:

备考时请重点掌握以下核心概念：

More similar DNA or protein sequences indicate a recent common ancestor.
Mutations accumulate at a roughly constant rate, enabling molecular clocks.
Cytochrome c, haemoglobin and rRNA are model molecules for comparison.
Immunological techniques measure antibody-antigen precipitation to compare proteins.
mtDNA and cpDNA offer advantages such as maternal inheritance and high copy number.
Phylogenetic trees are built using alignment and maximum parsimony.

DNA或蛋白质序列越相似，说明共同祖先越近。
突变以大致恒定的速率积累，使得分子钟成为可能。
细胞色素c、血红蛋白和rRNA是比较的经典分子。
免疫学技术通过测量抗体-抗原沉淀来比较蛋白质。
mtDNA和cpDNA具有母系遗传和高拷贝数等优点。
系统发育树通过序列比对和最大简约法构建。

Remember that all living organisms share a common ancestor because of the universal nature of the genetic code and core metabolic pathways. Therefore, any gene or protein that performs a fundamental function can be used to trace the history of life on Earth.

请记住，由于遗传密码和核心代谢途径的普遍性，所有生物体共享一个共同祖先。因此，任何执行基本功能的基因或蛋白质都可以用来追溯地球生命的历史。

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Molecular Comparisons Between Species and Evolutionary Relationships | 物种间分子比较与亲缘关系