New Volvocalean phylogeny

My postdoc makes fun of me for having a lousy memory. Not long ago she showed me a paper about microRNAs, and I said I hadn’t read it. She responded, “Yes you have; you blogged about it!” The other day we were discussing the use of antibiotics to prevent bacterial contamination, and I said I thought I might have done that at one time. She told me I had, it was ampicillin, and the concentration.

I’ve been blogging for nearly four years now, and I’ve published well over 400 posts. So I’ve learned that before I sink a bunch of time into writing a new blog post, it’s worth a quick search to make sure I’m not going to repeat myself. When a new paper from Takashi Nakada and colleagues popped up in my Google Scholar alerts, I didn’t immediately realize that I had already written about it. That post was mainly about a new analysis by Thomas Pröschold and colleagues, with the Nakada trees serving as a point of comparison. The new paper is worth its own post, though.

A group of researchers from Keio University have published a new analysis of evolutionary relationships among green algae in the order Volvocales. Takashi Nakada, Yudai Tsuchida, and Masaru Tomita inferred relationships using one nuclear gene and five chloroplast genes.

Nakada et al. 2019 graphical abstract

Graphical abstract from Nakada et al. 2019 showing Chlamydomonas pila as sister to the multicellular volvocine algae (Tetrabaena, Gonium, Volvox).

Previously, I focused on the monophyly of the multicellular volvocine algae, i.e. the Tetrabaenaceae, Goniaceae, and Volvocaceae (TGV). The multigene analysis shown above supports monophyly, although the support values for the critical node are not shown (meaning that the Bayesian posterior probability is <0.90 and the bootstrap proportions are <50%). Similarly, the new phylogeny doesn’t do much to resolve the backbone relationships within the Volvocaceae. There are differences from previous analyses that would be important if true, specifically in the positions of Volvox globator (the sole representative of Volvox section Volvox) and of Yamagishiella (which appears as part of an isogamous clade rather than sister to the anisogamous/oogamous Eudorina/Pleodorina/(most) Volvox clade). Neither of these differences is well supported, though, which is typical; most published phylogenies provide poor support for these relationships.

Nakada et al. 2019 Fig. 2

Figure 2 from Nakada et al. 2019. Bayesian phylogenetic tree of core-Reinhardtinia based on combined 18S-atpB-psaA-psaB-psbC-rbcL gene sequences. Corresponding posterior probabilities (≥0.90; left) and bootstrap proportions (≥50%) from maximum likelihood (middle) and neighbor-joining (right) analyses are shown next to the branches. Branch lengths and scale bars represent the expected number of nucleotide substitutions per site. Metaclades (MC; 1.00 posterior probabilities).

The main point of the new paper, though, is the close relationship between the multicellular volvocine algae and Chlamydomonas pila. The critical node for this relationship is is supported by a high Bayesian posterior probability (1.00) but crappy bootstrap values (55% for maximum likelihood and <50% for neighbor joining). The authors did do some analyses with fewer taxa to test this relationship, and those trees did have better support, but they also changed other relationships.

Correctly identifying the closest unicellular relative of the multicellular volvocine algae is critical for reconstructing the first steps in the transition to multicellular life. This is far from the first time that other species of Chlamydomonas and some of Vitreochlamys have been implicated. I’m not aware of any previous phylogeny that includes Chlamydomonas pila, but Chlamydomonas debaryana (for example) is usually closer when it is included.

I wouldn’t say that the evolutionary relationships in this group are fully settled at this point; the particulars vary among authors, depending on the gene(s) analyzed, and even depending on the method of phylogenetic inference. Even the monophyly of the multicellular species has been called into question, though I think it’s definitely too early to be confident in that conclusion. Right now it seems that Chlamydomonas pila is the best contender for the sister species to the multicellular clade, and almost certainly a closer relative to Volvox and co. than Chlamydomonas reinhardtii. As the authors point out, this makes C. pila a good candidate for whole-genome sequencing. The closer a relative to the multicellular group we can find, the better we can resolve which changes are specific to the multicellular clade.


Stable links:

Nakada, T., Tsuchida, Y. & Tomita, M. 2019. Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae). Mol. Phylogenet. Evol. 130, 1–8. doi: 10.1016/j.ympev.2018.09.013

Undergraduate summer internships at the Danforth Center

This is an unbelievable opportunity: an NSF-funded, paid summer internship at the Donald Danforth Plant Science Center in St. Louis. Ru Zhang is at the Danforth Center. Jim Umen is at the Danforth Center. The Fourth International Volvox Conference was at the Danforth Center. If you’re an undergraduate and you think you might want to study Volvox or Chlamydomonas (or plants), this would be a great way to get started.

Danforth Internship

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Volvox newsletter

Volvox newsletter cover

As David Kirk pointed out, what we normally call the First through Fourth International Volvox Meetings are really about the fifth through eighth, as they were preceded by several meetings in the ’70s. The very first meeting was hosted by David and Marilyn Kirk at Washington University in St. Louis. Richard Starr, then at Indiana University, reported on the meeting in the first Volvox Newsletter (Dr. Starr would later move to the University of Texas, and his strains would form the beginning of the UTEX Culture Collection, which is still in operation).

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More Volvox correspondence

I previously corresponded with a science teacher in India, who wrote me with some questions about Volvox. After our initial exchange, my correspondent wrote

Can you please name if there is any unicellular colonial microorganism found?

I asked for clarification and received this reply:

I read about colonial organisms being unicellular and multicellular. Few people think Volvox as colonial organism which is unicellular while Phylum Bryozoa has colonial organisms which are multicellular. The confusion started here. What are colonial microorganisms really? If they are unicellular and multicellular why are they called as colonial then? Bacteria being unicellular which form colonies thought Can bacteria be called as colonial organism? I tried to look for the same but I have not found something solid which says bacteria can be called as colonial organisms. I want to explain colonial organisms to children and don’t want to provide wrong information.

Can you please help in understanding do colonial unicellular microorganism exist? I asked one of the microbiologist I know in here she is also not clear with the concept or probably I might have read something wrong. Need guidance.

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Mary Agard Pocock

Alexey Desnitskiy, Stuart Sym, and Pierre Durand have published a new paper in Transactions of the Royal Society of South Africa recounting the contributions of South African phycologist Mary Agard Pocock to Volvox research [full disclosure: Pierre Durand and I were labmates in Rick Michod’s lab at the University of Arizona for a time, and Alexey Desnitskiy is a friend and collaborator].

Pocock, who defended her Ph.D. in 1932, made careful observations of both sexual and asexual development in several species of Volvox that she collected in southern Africa: V. africanus, V. capensis,V. rousseletii, and V. gigas (which she originally described). For some of these species, hers are still the only detailed descriptions of their ontogeny:

Pocock studied almost all aspects of asexual and sexual development in several African Volvox species, with the exception of sexual differentiation control…Pocock’s data on embryonic inversion in V. africanus, V. capensis, V. gigas and V. rousseletii retain their importance today. Her description of inversion during asexual development in V. africanus and V. capensis remains the only detailed study of this process in these two species and her observations of embryonic inversion in V. gigas and V. rousseletii were corroborated almost 40 years later. [references omitted]

Pocock 1933 Fig. 2L-O

Figure 2L-O from Pocock 1933. Inversion in Volvox gigas.

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I was in Canada

I have been disloyal to the fierce roller. After grad school, I stepped away from Volvox for a couple of years to do a postdoc with Michael Doebeli at the University of British Columbia. I thought I was going to transition to mathematical modeling, and Dr. Doebeli and I did do a bit of that together. I also got my first exposure to next-generation sequencing in his lab. I eventually returned to the fold, but during my time in Canada I wasn’t paying much attention to the Volvox world.

As a result, I missed Jerry Coyne’s coverage of the Volvox genome, which was published in 2010, just as I was discovering Jericho Beach, enjoying cheap sushi, and struggling to understand adaptive dynamics.

What does it take to become multicellular?

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CRISPR/Cas9 mutagenesis in Volvox

Researchers in Stephen Miller’s lab at the University of Maryland, Baltimore County have successfully used CRISPR/Cas9 to knock out several developmentally important genes in Volvox carteri. CRISPR/Cas9 is a relatively new technology that allows heritable mutations to be introduced into living cells at specific locations within the genome.

This advance was announced in a new paper in The Plant Journal by José A. Ortega-Escalante, Robyn Jasper, and Stephen M. Miller (Jasper and Ortega-Escalante are listed as equal contributors). They were able to transform wild-type V. carteri with inversion-deficient and somatic-regenerator mutations, and they transformed somatic regenerator mutants with a gonidialess (no specialized reproductive cells) mutation.

I have never used CRISPR/Cas9, and I don’t know as much about it as I should, so I’m sure any explanation I gave would be riddled with errors. Here’s someone who seems to know what she’s talking about:

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Repost: Message from David Kirk

After last week’s sad news that one of the founding fathers of Volvox research, David Kirk, had passed away, I thought it would be relevant to repost a message he sent a couple of years ago. The modern series of Volvox meetings started in 2011 in Arizona, and we’ve been calling them the First through Fourth International Volvox Conferences, with the Fifth scheduled for July 26-29, 2019. Dr. Kirk wrote in with some interesting historical insight about Volvox meetings that long preceded the current series:

I got an email out of the blue from David Kirk, and I thought some of it would be of interest. Dr. Kirk is one of the biggest names in Volvox research: he carried out much of the developmental genetics that forms the foundation of our field, he literally wrote the book on Volvox evo-devo, and my impression is that most of the PIs currently studying Volvox spent time in his lab as students and postdocs.


The email was prompted by the meeting review from the 2015 meeting in Cambridge (he liked it, whew! :-D), and he said that he’s looking forward to the 2017 meeting in St. Louis. The email also had a footnote with some interesting information, which I quote here with Dr. Kirk’s permission:

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Are the multicellular volvocine algae monophyletic?

One of the strengths of the volvocine algae as a model system is that they span a range of sizes and degrees of complexity. Sizes range from tens of microns to a couple of millimeters, cell numbers range from one to 50,000 or so, some species do and some don’t have cellular differentiation, and some do and some don’t undergo inversion during development. This variation makes the volvocine algae ripe for comparative analyses, which I and many others have done. It also allows many of the intermediate steps between unicellular and complex multicellular life to be identified, as David Kirk did in his “twelve-step” paper.

The volvocine algae have clearly taken some of those steps more than once. Cellular differentiation, for example, has evolved at least three times, in the genus Astrephomene, in the so-called Volvox section Volvox (a.k.a. Euvolvox), and in the lineage that includes Pleodorina and the other Volvox species. One thing they seem to have only done once, though, is to evolve multicellularity itself.

There have been dozens of studies addressing the evolutionary relationships among various species of volvocine algae. Most have been from Hisayoshi Nozaki’s lab, though I and many others have weighed in as well. Nearly all of them, at least those that address the topic, agree that the three families that make up the multicellular volvocine algae–the Tetrabaenaceae, Goniaceae, and Volvocaceae–uniquely descend from a common ancestor. In other words, the multicellular volvocine algae are monophyletic.

Three important cladistic terms are used to summarize the evolutionary relationships among a group of species. If all of the members of the group descend from a common ancestor, and nothing else descends from that ancestor, the group is called monophyletic. Mammals, for example, are monophyletic. A monophyletic group is also called a clade. If all group members are descended from a common ancestor, but so are some non-group members, the group is called paraphyletic. Reptiles, for example, are paraphyletic, because there is no clade that includes all reptiles that doesn’t also include birds. The word ‘paraphyletic’ should nearly always be followed by ‘with respect to’: reptiles are paraphyletic with respect to birds.

The bottom of the barrel, in terms of evolutionary relationships, is polyphyly. A group is considered polyphyletic if its members don’t share a recent common ancestor at all, in other words, if they have multiple evolutionary origins. Flying animals are polyphyletic. Algae are polyphyletic. The genus Volvox is polyphyletic. Polyphyletic taxa are the scum of the phylogenetic Earth. Telling a taxonomist that a group she has named is polyphyletic is a deadly insult.

The prevailing view of volvocine evolutionary relationships is that the family Volvocaceae is sister to the Goniaceae (that is, each is the other’s closest relative), and the Tetrabaenaceae are sister to the Volvocaceae + Goniaceae. Two new papers infer relationships among volvocine algae and their unicellular relatives, and one of them challenges the view of multicellular monophyly.

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