More coverage of the Tetrabaena genome

Tetrabaena socialis

Tetrabaena socialis. Image by Hisayoshi Nozaki and Yoko Arakaki.

I reported last week on the publication of the Tetrabaena socialis nuclear genome by Jonathan Featherston and colleagues. Several other sources have reported on their work as well. The press release from University of Witwatersrand was reprinted by Eurekalert, Brinkwire, Archaeology News Network, and others. Shorter versions are at Worldwide News, The Everyday News, and Times Higher Education. The story has also been reported in Spanish, Russian, Czech, Vietnamese, and, of course, Afrikaans.

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Clues to the evolution of multicellularity from Tetrabaena

One development I’m excited to see among the Volvox community is an increased focus on Tetrabaena, one of the smallest and simplest of the colonial volvocine algae. The one species in this genus, Tetrabaena socialis, was classified as Gonium until 1994, when Hisayoshi Nozaki and Motomi Itoh revised it not only to a new genus but a new family, the Tetrabaenaceae.

Nozaki & Itoh 1994 Fig. 10

Figure 10 from Nozaki & Itoh 1994. Summary of the phylogenetic relationships within the colonial Volvocales inferred from cladistic analysis based on morphological data.

Their classification was based on morphological characters, but the backbone relationships, Tetrabaenaceae sister to Goniaceae + Volvocaceae, have subsequently been supported in several independent analyses using genetic data.

In 2013, very much to my surprise, Yoko Arakaki and colleagues showed that the (typically) four cells of Tetrabaena are connected by cytoplasmic bridges (this means that some of the ancestral character state reconstructions I did in grad school need to be revised). Their detailed analyses of Tetrabaena morphology and development are a valuable resource for comparative studies.

Now, in addition to the morphological data, we also have complete sequences for both organelle genomes (mitochondria and chloroplast) and for the nuclear genome. Jonathan Featherston and colleagues published the organelle genomes in 2016, and their new paper in Molecular Biology and Evolution describes the nuclear genome.

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More evidence for co-option in the evolution of soma

One of the reasons Volvox was developed as a model organism was that it has the minimum number of cell types something with cellular differentiation can have: two. This property focuses investigations of cellular differentiation in a way that an organism with many cell types could not. In describing their move from studying avian and mammalian models to studying Volvox, Marilyn and David Kirk said,

The thing that appealed to us most about V. carteri – in addition to the genetic accessibility that Starr (1970) had already demonstrated – was the fact that it presented the germ-soma dichotomy in such a clear and simple form. Each asexual adult (or “spheroid”) of V. carteri contains only two cell types: small, biflagellate somatic cells, and large asexual reproductive cells, called gonidia (figure 1). The somatic cells are mortal; once they have provided the organism with motility for a few days they die. The gonidia, in contrast, are potentially immortal; each mature gonidium acts as a stem cell, dividing to produce a juvenile organism containing a new cohort of gonidia and somatic cells. No one has ever found a way to make wild-type somatic cells divide, but the only way to prevent gonidia from dividing is by withholding energy or poisoning them. Who could ask for a clearer presentation of one of the central issues of developmental biology: how are cells with extremely different phenotypes produced from the progeny of a single cell?

Kirk & Kirk 2004 Fig. 1

Figure 1 from Kirk & Kirk 2004. A young adult spheroid of V. carteri consists of thousands of small, biflagellate somatic cells that are embedded at the surface of a transparent sphere of extracellular matrix, and about 16 large asexual reproductive cells, called gonidia, that are located just internal to the somatic cells.

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Some responses to “A cautionary tale on reading phylogenetic trees”

PLoS ONE logo

Back in September, I complained that a PLoS ONE article purporting to provide “valuable insight into the evolution of eukaryotes” contained substantive problems that should have been caught during the peer review process (“A cautionary tale on reading phylogenetic trees“). The problems are so serious that, in my opinion, they render the bulk of the results invalid.

There were also numerous problems with the interpretation of those results, mainly stemming from misunderstandings about what kinds of information phylogenetic trees represent:

Some of these problems are just rhetorical, but some of them are substantive, and this is the real problem. A failure to understand that phylogenies represent sister group relationships has led to incorrect interpretations of evolutionary relationships, such as that the outgroup is more closely related to one ingroup clade than another, that the sister of one clade is a ‘link’ to another clade, and that a single branching event can have a bunch of different divergence times.

I later admitted, in response to criticism from a reader, that I may have been overly pedantic in pointing out some of the rhetorical problems (“A valid point“). In this post, though, I’m going to focus on the substantive problems and respond to a couple of comments to the original post.

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Exxon still loves Volvox

I hope Exxon’s scientists know more more algal taxonomy than their ad team. We’ve seen before that they don’t know the difference between Chlorophyte green algae and cyanobacteria (Exxon loves Volvox). Some of the things they’ve lumped together in that video are more distantly related than humans are to mushrooms.

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MicroRNAs in Chlamydomonas

One of the biggest changes in evolutionary theory in the late 20th century was the growing appreciation for the central role of changes in gene expression in macroevolution. Developmental genes, especially Hox genes, turned out to be remarkably conserved across lineages that diverged over half a billion years ago. The subsequent huge changes in morphology were more often due to changes in when and where those genes were expressed than to changes in the coding sequences of the genes themselves.

Even more recently, an entire new class of regulatory mechanisms was discovered and found to be important in developmental processes. MicroRNAs (miRNAs) are short (21-24 nucleotides) sequences of RNA that reduce gene expression by promoting the breakdown of messenger RNAs (mRNAs) and by repressing translation of mRNAs into proteins. We have only known that microRNAs even existed since the early 1990’s, and their importance in gene regulation and development wasn’t appreciated until the 2000’s.

Although they are structurally similar, plant and animal microRNAs repress gene expression through very different mechanisms. A new paper by Betty Y-W. Chung and colleagues in Nature Plants shows that the regulatory mechanisms of Chlamydomonas microRNAs have both striking similarities and important differences with animal miRNAs:

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A trio of algal biophysics talks

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The 70th Annual Meeting of the American Physical Society Division of Fluid Dynamics, November 19–21, 2017 in Denver, Colorado, will include a few talks about Volvox and Chlamydomonas motility. Timothy Pedley from Cambridge will present “An improved squirmer model for Volvox locomotion“:

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Non-model model organisms

Jim Umen, the lead organizer of the upcoming Volvox meeting, has written a section for a new paper in BMC Biology, “Non-model model organisms.” Like all of the BMC journals, BMC Biology is open access, so you can check out the original.

The article surveys organisms that, while not among the traditional model systems, have been developed as model systems for studying particular biological questions. The paper has an unusual format, with a discrete section devoted to each species, each written by one or two of the authors. Aside from Volvox, there are sections on diatoms, the ciliates Stentor and Oxytricha, the amoeba Naeglaria, fission yeast, the filamentous fungus Ashbya, the moss Physcomitrella, the cnidarian Nematostella, tardigrades, axolotls, killifish, R bodies (a bacterial toxin delivery system), and cerebral organoids (a kind of lab-grown micro-brain).

Dr. Umen presents Volvox and its relatives as a model system for understand the evolution of traits related to the evolution of multicellularity:

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