遗传 进化与生态学 2 - Phylogenies

本章的内容是系统发生树/演化。本文集的这一部分是遗传、进化与生态学 Genetics, Evolution, and Ecology. 这门课理论上建议在阅读完文集的第一部分的内容之后再开始学习，但基础不足的朋友也可以尝试阅读喔~

这一部分的主要内容均来自 Prof. Angela J. Roles 的课程，因此本文集的这一部分均不会标记为原创。但由于文本来源不清晰，UP主还是一个字一个字码出来的文章，本文禁止非授权的转载，谢谢！

封面图：https://www.researchgate.net/profile/Thomas_Holtz/publication/40662863/figure/download/fig2/AS:670703217041421@1536919516720/continued-Previously-proposed-phylogenies-of-theropod-relationships-Taxonomy-of-listed.png

Lesson 2: Phylogenies 

    Last Lesson: classification systems, also called taxonomy. This is the system that we use to name species.

    But how do we talk about common ancestry and relationships among species? How do we identify what grouping constitutes a species?

[1] Structure of a Phylogeny

▸PHYLOGENETICS: the study of the evolutionary relationships among biological units. Phylogenetic trees (or phylogenies) graphically represent these relationships.

    - In addition to the morphology-dependent methods of classical taxonomy, modern phylogenetics also considers genetic data;

    - Both morphology and genetics reflect common ancestry;

    - Both are vulnerable to convergence: when organisms are similar not due to common ancestry but due to similar ecological pressures yielding common solutions.

What’s a phylogenetic tree?

This phylogeny depicts the relationships of the Domains (Bacteria, Archaea, and Eukarya), each represented by multiple types of organisms at the tips.

You can see that everything labeled Archaea shares a single common ancestor. Think about how this relates to the taxonomic ranks from last time.

Anatomy of a phylogeny

▸Terminal taxa (tips) usually represent extant taxa (currently living).

    - A tip may be a single species (or taxon) or a group of taxa.

    - Sometimes tips are extinct taxa, such as fossils.

▸Nodes (or branch points) and branches represent ancestors.

    - They are also divergence points;

    - The point at which two new species evolved (diverged) from a shared ancestor. 

Time in a phylogeny

▸Time is implied in the tree, here only relative time.

▸Tips are the present day. Movement along a branch away from the tip is going back in time.

▸Imagine that each point along each branch represents an ancestor of the terminal taxa.

▸The oldest node on the tree is the basal node. It is the common ancestor of all the taxa on the tree.

▸Sometimes branch lengths estimate amount of genetic difference between taxa or absolute time since divergence (calibrated with fossils).

Topology and clades

    Branches can rotate around nodes: The order of taxa at the tips is not meaningful, relationships among taxa depend only on the branch order.

Defining clades on trees

    A clade is a group of organisms that includes a single ancestor and all of its descendents. Clades represent unbroken lines of evolutionary descent.

▸Each group highlighted in the image at the right forms a valid clade

▸Note that Crocodiles are part of two clades.

Clades are monophyletic groups

    ▸Monophyletic groups are composed of an ancestor and ALL of the descendants of that

ancestor.

    ▸Thus, we see that Reptiles, as commonly defined, is not a monophyletic group (why not?)

    ▸However, we see that Dinosauria is a monophyletic group (so long as it includes birds!)

[2] Using Phylogenies

What do you use a phylogeny for?

▸Discovering the relationships among taxa;

▸Studying how traits evolve over time;

▸Identifying the source of infectious diseases such as SARS;

▸Determining the source of products suspected to be from protected, endangered taxa (such as rhino horn or elephant tusks).

When information transfer isn’t vertical:

▸Horizontal gene transfer (HGT): the exchange of genetic material between units, by non-reproductive mechanisms.

▸Important mechanism providing new genetic material to a lineage.

Phylogenies and the scientific method

▸Where do you think phylogenies fit into the scientific method? Why?

▸They are often considered to be hypotheses of evolutionary relationships.

▸Including additional taxa, using different characters, or different methods could change the hypothesized relationships.

Interpret with caution!

    ▸Sometimes, phylogenies can be misleading. Why? What can we do when creating phylogenies to reduce the chance that we are misled?

Consider this phylogeny for strains of the 2003 SARS virus outbreak.

▸We’d conclude SARS in humans is most closely related to civets, then to bats. (Note: recombination isn’t shown on phylogenies.)

▸What if we used a different part of the viral genome to make a phylogeny?

▸What if we included SARS viruses from other mammals?