p1: The idea of this course is not to learn how to make phylogenetic trees,
p1: but to be able to read them as well to see how they can be used to better understand
p1: the evolution of forms and the evolution of development in different lineages.
p1: The theory of evolution explains the fundamental unity of the living and
p1: also the evolution of forms in different lineages over the course of time.
p1: The objective of a phylogenetic tree is to represent a hypothesis about relationships
p1: in the form of a tree. It's obtained thanks to research
p1: on homologous characters in the species of interest, which will be the group of study.
p1: These characters can be morphological or molecular.
p1: To be able to read a phylogenetic tree, it's necessary to know some basic vocabulary.
p1: The first things to identify are the leaves or terminal taxons.
p1: They correspond to one species, or population, or a lineage.
p1: In the case of molecular phylogeny, it's about genes
p1: as you can see here, but sometimes fossils can be used in other analyses.
p1: Branches correspond to successions of theoretical ancestors.
p1: Note that other features here are only meant to regroup branches together
p1: but do not have meaning. And besides, it's possible to represent branches in that way.
p1: The nodes are also an important element that indicate the placement of the last
p1: hypothetical common ancestor or the most recent hypothetical common ancestor
p1: before a divergence. Note that the rotation around the node
p1: doesn't change the relationship between taxons.
p1: It's also necessary to spot a particular branch that is considered to be the most
p1: ancient of the tree. This is called the root,
p1: and it's usually identified thanks to the outgroup.
p1: The outgroup is a group located outside of the ingroup, but not too far in order
p1: to share characters together with the ingroup.
p1: The outgroup gives us the sense of evolution polarising the tree, and
p1: giving a sense of time. If we don't have this polarization, the analysis produces
p1: a network, and not a tree.
p1: To describe a tree and to compare nodes and branches, it's necessary to compare
p1: them with an adapted vocabulary. If we want to compare node 1 with node 2,
p1: we will say that node 1 is more internal, deep, or basal than node 2.
p1: In comparison, we will say that node 2 is more external or superficial than node 1.
p1: In one phylogenetic hypothesis, we need to search for a group that diverts from
p1: an ancestor and includes the totality of descendants.
p1: This group is characterised by the acquisition of one or several characters
p1: in a derivative form, implicating a trans- formation, and is only shared by this group.
p1: For example, the cnidocytes of cnidarians.
p1: This group is called a monophyletic group or clade which is only valid in systematics.
p1: It will be necessary to differentiate these groups from the groups sometimes used
p1: in the literature that are based on the distribution of characters in the
p1: ancestral state such as fish, reptiles, and which are paraphyletic groups
p1: and not used in current systematics.
p1: The group based on the distribution of independently acquired characters
p1: and which are therefore convergent such as seaweed is called a polyphyletic group,
p1: which is the worst possible group in systematics!
p1: Here you can see trees coming from different phylogenetic methods.
p1: In the cladistic method, only the relationship is indicated,
p1: and the length of branches is not indicative of evolutive divergence.
p1: In other methods, it's possible to show this divergence.
p1: An important notion in phylogeny is to know the node robustness.
p1: Indeed, we are looking for indicators of reliability in the observed topology.
p1: For this, there are often several indications with each node.
p1: Bootstrap is the indication calculated by a method of reanalysing the data and which
p1: estimates the percentage of time when this node is found.
p1: They consider that a node under 60 or 80% is not robust.
p1: In a Bayesian analysis, another indicator that is frequently used
p1: is called the posterior likelihood value.
p1: This value should not be less than 0.9.
p1: It's often interesting to identify sister groups. The monophyletic group the
p1: most related to another monophyletic group which together form a monophyletic group
p1: are particularly useful to compare in order to understand the evolution of characters,
p1: notably in those who appear in the course of development.
p1: It's also possible to estimate the age of node divergence.
p1: The notion of dating notes is based on the principle of the molecular clock,
p1: where mutations appear with some regularity over time. Of course,
p1: it's not possible to directly use the divergence as proportional to time,
p1: but it's possible to estimate the age of a node by adapted statistical methods.
p1: This method is based on calibration by dating one or several nodes,
p1: often with fossils. Now let's look at some examples.
p1: When we look at a phylogeny of eukaryotes, we can identify many lineages.
p1: You can locate animals, which constitute a monophyletic group,
p1: but also algae or fungi, which are polyphyletic.
p1: On the other hand, among algae there are
p1: monophyletic groups too, such as brown or red algae.
p1: We can see in this example of metazoan phylogeny some instances of synapomorphy
p1: for important phyla: bilateral symmetry and the three embryonic leaves forming a coeloma
p1: in bilaterians, cnidocytes in cnidarians as we have seen,
p1: the spicules in sponges, radula in mollusks, or the articulated legs of arthropods.
p1: More examples will be provided in the different DigitalMarine modules.
p1: However, some important pending questions remain.
p1: The base of the metazoan tree remains a domain that is still subject
p1: to contradictory hypotheses. Why is the phylogeny hypothesis important?
p1: Well, if the phylogeny changes, the interpretation of the evolution of
p1: characters will change, as well as our understanding of the modification
p1: of developmental processes.
p1: You now should have the basics for how to read a phylogenetic tree as well as
p1: understand how it can be used to explore the evolution of forms in research.
p1: In the next chapter we'll look more specifically at my favorite group: the crustaceans.