p1: In the last chapter, we've seen basic features of amphioxus' morphology
p1: life cycle and development. But you still don't know why amphioxus is so interesting
p1: and why amphioxus is our favourite animal.
p1: As you've seen in the 1st chapter, zoologists of the 19th century were very
p1: interested by amphioxus because they were thinking it was the missing link
p1: between invertebrates and vertebrates.
p1: But amphioxus is an extant species not a fossil so it cannot be this missing link.
p1: However, the phylogenetic position of amphioxus among chordates is very important,
p1: and is one of the characteristics that make amphioxus very good model for us in the lab
p1: so in this chapter we will see what are the phylogenetic relationships between
p1: the different chordate clades, and at the end of this video you should be able
p1: to place all the groups of chordates ﻿onto a phylogenetic tree.
p1: So now let's go together to the classroom.
p1: Cephalochordates, amphioxus -you have one- belongs to the chordate clade together
p1: with vertebrates, so here you have a nice teleost fish as a vertebrate and
p1: together with tunicates also called urochordates.
p1: So for a long time, it was thought that cephalochordates were more closely
p1: related to vertebrates than tunicates.
p1: Indeed, if we look at the morphology, also, if we look at the tadpole of
p1: an ascidian, a tunicate, it looks like a tadpole of an amphibian, which is
p1: a vertebrate.
p1: At the adult stage, tunicates resemble
p1: much less vertebrates than do cephalochordates.
p1: Moreover, you will see in the tunicates course
p1: that embryonic development modalities are very different between
p1: tunicates and the other chordate groups. For example, in amphioxus
p1: as in vertebrates, development is mainly regulative.
p1: Whereas in tunicates it is a mosaic development, mainly mosaic.
p1: During early development in amphioxus as in vertebrates, there is a special
p1: territory that is formed, which is called the organiser.
p1: This is the Spemann organiser in amphibians
p1: and this structure is very important, as it is able for example, when it is
p1: grafted onto a host embryo to induce the formation of a secondary body axis.
p1: So this structure will control the formation of the main axis of the embryo
p1: in cephalochordates,
p1: in vertebrates,
p1: whereas in tunicates there is no organiser.
p1: Another difference in amphioxus as in vertebrates, muscles and other structures
p1: of the body are derived from blocks of paraxial mesoderm that are forming
p1: during development,
p1: which cause somites.
p1: These somites form from the anterior part to the posterior part,
p1: and they form through a process, which is called somitogenesis, in amphioxus
p1: and in vertebrates.
p1: In tunicates there are muscles that are forming during development,
p1: and muscles of the tail form some blocks, but they are not forming through
p1: the formation of somites and through somitogenesis.
p1: So, the morphology between cephalo- chordates and vertebrates is very similar
p1: and the developmental modalities are also very similar between these two groups
p1: of chordates. Now let's see what we can tell about the genome.
p1: So another argument, which supports the fact that cephalochordates would be more
p1: closely related to vertebrates and tunicates comes from data of the genome.
p1: In fact, amphioxus cephalochordates have a prototypical chordate genome
p1: whereas tunicates have a very derived genome, and vertebrates have a duplicated
p1: genome, so let's see the story of the duplicated genome of vertebrates first.
p1: In the 70s, a Japanese-American geneticist called Susumu Ohno
p1: proposed in his book "Evolution by Gene Duplication" that morphological novelties
p1: could be the result of genes or genome duplications,
p1: and he proposed that during the evolution of the vertebrate clade there were two
p1: whole genome duplications.
p1: For many years, researchers tried to find some arguments to decipher if
p1: this hypothesis, which is called the 2R hypothesis, was true
p1: by comparing the number of isozymes, genes, and paralogues between vertebrates
p1: and non-vertebrate species. However, the real answer to the question "is the
p1: hypothesis true?" came from the sequencing of the whole genome
p1: of the tunicate Ciona intestinalis.
p1: And when the researchers compared this genome to the genomes of vertebrates,
p1: they were able to show that indeed there were two whole genome duplications
p1: at the base of the vertebrate lineage.
p1: What we are sure of is that there was at least
p1: one whole genome duplication here at the base of the vertebrate history
p1: before the divergence between cyclostomes, which are the lampray and hagfish, so
p1: vertebrates without jaws, jawless vertebrates, and the gnathostomes,
p1: which are the vertebrates with jaws. So one duplication here, and for the 2nd one,
p1: we don't know if this duplication occurs here just after the first one
p1: or if it occurred
p1: here
p1: after the divergence between cyclo- stomes and gnathostomes.
p1: What is very interesting is that after this hypothesis,
p1: another hypothesis was mentioned by the group of Axel Meyer in Germany
p1: in the 90s, which was that there was an additional whole-genome duplication in
p1: the lineage of the teleosts, so the teleost fish.
p1: And in fact, it was also shown after the sequencing of whole genomes of several fish
p1: that indeed there was another duplication here
p1: at the base of the evolutionary history of the teleost lineage.
p1: What is important to notice here is that
p1: we can observe that cephalochordates and tunicates have an unduplicated genome
p1: compared to vertebrates.
p1: So, let's see now other things about genome and gene contents.
p1: So amphioxus not only has an unduplicated genome,
p1: but in the genome of amphioxus we can also find all the genes that were thought
p1: to have been present in the ancestor of chordates.
p1: If we look at the example of the hox cluster we can see that in amphioxus there is only
p1: one hox cluster with all the 14 genes retained.
p1: If we look at vertebrates, so as we've seen before, there were several genome
p1: duplications so there are several hox clusters for example, four hox clusters
p1: in mammals.
p1: and in each cluster some genes were lost.
p1: Now, if we look at tunicates, the hox cluster was completely broken and
p1: many, many genes were lost.
p1: The worst case is the case, not the worst but extreme
p1: case is the hox cluster in the tunicate Oikopelura dioica
p1: which in fact, is no more a cluster. It is completely destroyed.
p1: Another example comes from the homeobox gene families.
p1: So homeobox are genes that code for transcription factors that have a
p1: homeobox DNA binding domain,
p1: and if we have a look at all the family members, we can see that they were
p1: thought to have been present in the chordate ancestor.
p1: We can see that in vertebrates some of these members were lost.
p1: If we look at tunicates we see that they've lost even more members of this family.
p1: Now, if we look at amphioxus we can see that the genome of amphioxus contains
p1: all the members that were thought to have been present in the genome of
p1: the chordate ancestor.
p1: So this is the case of the homeobox family but if we now have a look at another
p1: gene family, like the tyrosine kinase family, it is the same story.
p1: So tyrosine kinases are proteins that posess a tyrosine kinase domain
p1: and other domains, so there are different sub-families inside this family.
p1: Some of the groups were lost in diploblastic animals like Nematostella.
p1: Some of the members were lost in protostomes like Drosophila or
p1: C. elegans.
p1: Some genes were also lost in vertebrates. However, in amphioxus we can observe that
p1: the genome contains at least 1 member of each of the sub groups of the
p1: TK superfamily.
p1: And this is also the case with most of the gene families that were studied so far,
p1: so amphioxus has a non duplicated genome and it has conserved all the genes
p1: that we thought were present in the chordate ancestor.
p1: Okay, so from the developmental, morphological, and genomic POV
p1: it seems that cephalochordates are more closely related to vertebrates than
p1: tunicates, but is it true? Do we have arguments against this hypothesis?
p1: Well in fact we might have some morph ological arguments against this hypothesis.
p1: I don't know if you remember, but I told you that in cephalochordates there are no
p1: migrating neural crest cells.
p1: These cells are known in vertebrates and they correspond to the border of the
p1: neural plate, so this neural plate will roll to form the neural tube and the cells
p1: of the border will migrate into the embryo to form several kind of cells like the
p1: cartilage and some muscles of the head, like melanocytes, like peripheral nervous
p1: system cells, many different kinds of cells.
p1: In fact, it was proposed to call the migrating neural crest cells the 4th
p1: germ layer of vertebrates.
p1: So these cells are absent in amphioxus, and were thought to be absent in tunicates.
p1: But in 2004, the team of Bill Jeffrey using a species of ascidian
p1: with very big, with giant tadpole larvae
p1: were able to show that at least in this species there are indeed some cells that
p1: form in the border of the neural plate and that are able to migrate into the embryo
p1: to form some pigment cells. So these cells are﻿
p1: a little bit like neural crest cells of vertebrates.
p1: So if we consider this morphological characteristic, here we have migrating
p1: neural crest cells. Here we have also these cells or at least like.
p1: OK
p1: And here
p1: if we consider
p1: the first tree
p1: OK neural crest cells no NCC, no NCC
p1: Here, the outgroup
p1: Would be
p1: the Ambulacraria
p1: they don't have NCC OK so here we don't have
p1: and here we don't have so if we want to explain the evolution of this character
p1: the easiest way, the most parsimonious way to explain the appearance of this
p1: character would be that it appeared here.
p1: In the ancestor of vertebrates and tunicates.
p1: OK, so only one evolutionary step.
p1: If now we consider amphioxus as more closely related to vertebrates
p1: so in amphioxus we said
p1: no neural crest cells
p1: and in the outgroup
p1: no NCC
p1: the most parsimonious scenario here to explain
p1: What we can see nowadays in these extant spaces is that
p1: NCC appeared here in the ancestor of
p1: Vertebrates and tunicates which is now the ancestor of all the chordates
p1: and that the NCC character disappeared here in the lineage of cephalochordates.
p1: So here we have one evolutionary step.
p1: And here we have
p1: 2 evolutionary steps, so if we choose the most parsimonious scenario, we will
p1: decide to choose this one and in this one you can see that tunicates are more closely
p1: related to vertebrates. So this is taking into account only these
p1: morphological characteristics.
p1: Now in fact, the real answer to the question who is more closely related to vertebrates.
p1: The answer came from the sequencing of the genome of several tunicates, among
p1: which Ciona intestinalis and Oikopelura dioica and of many other species.
p1: Using phylogenetic tree reconstruction with this genomic data, which is
p1: called Phylogenomics,
p1: researchers were able to show that indeed in fact tunicates
p1: are more closely related to vertebrates than cephalochordates
p1: although they are very divergent in terms of genome, development, and morphology.
p1: So for a long time, it was thought that cephalochordates were more closely
p1: related to vertebrates than tunicates.
p1: Today, the generally accepted view of the evolutionary relationships between
p1: the different chordate clades is that tunicates are the sister group
p1: of vertebrates, whereas cephalochordates diverge before in the chordate clade.
p1: This is very important because this completely changed our view of how
p1: chordates evolved. Why?
p1: Here, with this tree, which was thought to be true before the sequencing of the
p1: whole genome of many species,
p1: it was thought that the vertebrate ancestor
p1: which is here in the tree was morphologically like a tunicate tadpole.
p1: OK? And that here we had another ancestor, the ancestor of vertebrates and
p1: cephalochordates was a little bit like cephalochordates, a vertebrate but simpler.
p1: If we now consider the accepted view
p1: of the phylogeny of chordates,
p1: the ancestor of all chordates is here,
p1: so this is the last common ancestor between
p1: cephalochordates and vertebrates, which means that the chordate ancestor
p1: was probably not like a tadpole of an ascidian but more likely it had a morphology
p1: that was quite close to the morphology we can see in amphioxus nowadays.
p1: Also amphioxus is not a fossil and evolved after the divergence with vertebrates,
p1: but probably here the chordate ancestor was
p1: a little bit like a vertebrate, but simpler.
p1: And tunicates
p1: derived a lot after the divergence with vertebrates.
p1: So this is very important for us and as you can see
p1: because of its morphological, developmental, genomic characteristics and because of its
p1: phylogenetic position in the tree of chordates, amphioxus is a very good proxy
p1: for the chordate ancestor and it's very interesting model to try to understand
p1: how the morphology and the genomes evolved in the chordate clade.
p1: Indeed, when we compare characteristics between amphioxus
p1: and vertebrates, if they are the same, we can make the hypothesis that
p1: these characteristics were already present in the ancestor of chordates.
p1: And if we find differences between both clades, we can have an idea on how specific
p1: morphological characteristics/features appeared in the vertebrate lineage.
p1: So this is why amphioxus is my favourite animal and this is why I use it in the lab.
p1: At the end of this chapter you should be able to place so different chordate clades
p1: in a phylogenetic tree and to draw the position of the genome duplication - the
p1: whole-genome duplication - that occurred during the evolutionary history of the
p1: different chordate lineages.
p1: See you soon for the next chapter.