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What is a Phylogenetic Tree -
How to look at a phylogenetic tree and determine which species are most related
1. Key points
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A phylogenetic tree is a diagram representing the evolutionary relationship between organisms. Phylogenetic trees are hypotheticals, not established facts. -
Branching patterns in a phylogenetic tree reflect the relationships of how species or other groups have evolved from a series of common ancestors. -
In a tree, two species are more closely related if they have a more recent common ancestor, and more distant if they have a more distant common ancestor. -
Phylogenetic trees can be drawn in various styles. Rotating a tree around its branch points does not change the information it carries.
2. Introduction
Most modern classification systems are based on the evolutionary relationship between organisms—that is, the phylogeny of organisms. Phylogenetic-based classification systems organize species or other groups in ways that reflect our understanding of how they evolved from a common ancestor.
In this article [1] , we will learn about phylogenetic trees, diagrams that represent evolutionary relationships between organisms. We'll see exactly what we can (or not!) infer from phylogenetic trees, and what it means for species to be more or less related in the context of these trees.
3. Anatomy of a tree
When we draw a phylogenetic tree, we represent our best hypothesis about how a group of species (or other groups) evolved from a common ancestor. As we'll explore further in our article on tree building, this assumption is based on information we gather about collections of species—such as their physical characteristics and the DNA sequences of their genes.
In a phylogenetic tree, species or groups of interest are at the tops of lines called branches. For example, the following phylogenetic tree shows the relationship between the five species A, B, C, D, and E at the end of the clade:
The pattern of branch connections represents our understanding of how species in the tree evolved from a series of common ancestors. Each branch point (also known as an internal node) represents a divergence event, or splitting of a group into two descendant groups.
在每个分支点处都有从该分支点派生的所有组的最近的共同祖先。例如，在产生物种 A 和 B 的分支点，我们会找到这两个物种最近的共同祖先。在树根正上方的分支点，我们会找到树中所有物种（A、B、C、D、E）最近的共同祖先。
下图显示了树中的每个物种如何将其祖先追溯到根上方分支点的最近共同祖先：
树中的每条水平线代表一系列祖先，一直延伸到其末端的物种。例如，通往物种 E 的线代表该物种的祖先，因为它与树中的其他物种不同。同样，根代表了一系列祖先，直到树中所有物种的最近共同祖先。
4. 物种关系判断
在系统发育树中，两个物种的相关性具有特定的含义。如果两个物种有更近的共同祖先，则它们之间的关系更近；如果它们的共同祖先更远，则它们之间的关系更远。
我们可以使用一种非常简单的方法来找到任何一对或一组物种的最近共同祖先。在这种方法中，我们从带有两个感兴趣物种的分支末端开始，然后在树中“向后走”，直到我们找到物种线会聚的点。
例如，假设我们想说是 A 和 B 还是 B 和 C 关系更密切。为此，我们将沿着树中两对物种的线向后移动。由于 A 和 B 在我们向后移动时首先会聚到一个共同的祖先，而 B 只会在其与 A 的交界点之后才与 C 会聚，因此我们可以说 A 和 B 比 B 和 C 更相关。
重要的是，有些物种的相关性我们无法使用这种方法进行比较。例如，我们不能说 A 和 B 是否比 C 和 D 更密切相关。这是因为默认情况下，树的水平轴并不直接表示时间。因此，我们只能比较发生在同一谱系（树根的同一条直线）上的分支事件的时间，而不能比较发生在不同谱系上的分支事件的时间。
5. 小技巧
您可能会看到以许多不同格式绘制的系统发育树。有些是块状的，就像下面左边的树。其他人使用对角线，例如右下方的树。您可能还会看到任何一种树都是垂直方向或侧翻的，如块状树所示。
The three trees above represent the same relationship between species A, B, C, D, and E. You might want to take a moment to convince yourself that this is the case -- that is, two trees with no branching pattern or recency in common have different ancestors. The same information in these seemingly different trees reminds us that it is the branching patterns (not the lengths of the branches) that are meaningful in a tree .
Another key point about these trees is that if you rotate the structure, using one of the branch points as the pivot, the relationships are not changed. So just like the two trees above show the same relationship despite their different formats, all the trees below show the same relationship between the four species:
All the trees we've seen so far have a clear branching pattern, with only two lineages (lineages) occurring at each branch point. However, you may see multi-branch trees, which means a branch point has three or more different species. Usually, this indicates that we don't have enough information to determine the branch.
6. The source of the tree
To generate a phylogenetic tree, many characteristics of the species or other groups involved are often compared and analyzed. These features can include external morphology (shape/appearance), internal anatomy, behavior, biochemical pathways, DNA and protein sequences, and even characteristics of fossils.
To build accurate, meaningful trees, biologists typically use many different features (to reduce the chance that any one imperfect piece of data will lead to a wrong tree). Still, phylogenetic trees are hypotheses, not definitive answers. The tree is revised and updated over time as new data becomes available and can be added to the analysis. Because DNA sequencing improves our ability to compare relationships between species.
References
Source: https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny
This article is published by mdnice multi-platform