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

“It was I who destroyed Ehrenberg’s theory”

Volvox globator

Volvox globator Ehrenberg (frontispiece of Julian Huxley’s The Individual in the Animal Kingdom, after A. Lang).

“The Diamond Lens” is a short story published by the Irish writer Fitz-James O’Brien in 1858. It describes the quest of an obsessed amateur microscopist for ever greater degrees of magnification, a goal for which he is willing to go to exceptional lengths. O’Brien was apparently known for mixing scientific themes with mysticism, and “The Diamond Lens” certainly fits this description. I won’t spoil it any further; interested readers can download the story for free (in several formats) from The Gutenberg Project.

As the narrator and protagonist becomes a proficient microscopist, he encounters Volvox:

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Convergence part 7: convergence in Volvox

Last year I wrote a series of posts on convergent evolution and misrepresentations of the history of the concept by proponents of intelligent design including Günter Bechly, Lee M. Spetner, Granville Sewell, and others. I didn’t intend for there to be a two-month gap before the final installment (nor am I sure this is the final installment), but here we are.

To quickly recap, I showed in the first three installments that

The Discovery Institute is producing a revisionist history. To hear them tell it, convergence is something that evolutionary biologists have either barely heard of or that they “invented” or “made up” to hide problems with the tree of life. Convergence “destroys the tree of life,” it “contradict[s] the [modern synthesis],” and it is “quite unexpected” to evolutionary biologists. All of that is a big, stinking pile of wrong. In reality, biologists since Darwin, and including Darwin, have always appreciated the importance of convergence, have written thousands of papers about it, and have included it in every evolutionary biology textbook I’m aware of.

I explained why the argument that convergence is evidence against common descent is daft, and I gave a spectacular example of convergent (or parallel) recruitment of life cycle genes in plants and brown algae. I also promised that I would write about convergent evolution in Volvox, which I have so far failed to do.

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A new way to follow Fierce Roller

For those of you who don’t use a feed reader, I have set up a Facebook page for Fierce Roller: facebook.com/FierceRoller. If this works the way I think it should, all you have to do is go there and hit the “Like” button, and you’ll get an alert each time I publish a blog post. If you do use a feed reader, you can follow the blog by adding freethoughtblogs.com/fierceroller/?feed=rss2.

Postdoctoral fellowship in the evolution of multicellularity

Thompson lab

Image from https://thethompsonlab.wordpress.com/.

The Thompson lab at University College London is looking for a postdoctoral researcher to study the evolution of multicellularity:

The Thompson lab, based at University College London, is seeking a Research Fellow to work on understanding how gene network heterogeneity affects the evolution of multicellular development.

Recently, we found that cell-cell variation in cell cycle position facilitates symmetry breaking during development, as it primes cells to respond to different differentiation cues (Gruenheit et al, Developmental Cell, 2018).

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Forest bathing baloney on Living on Earth

Forney Creek, GSMNP

Forney Creek, Great Smoky Mountains National Park.

I listen to NPR nearly every morning, and on Saturdays that means Living on Earth, at least on my local station. This Saturday I tuned in partway through a segment on “forest bathing,” also known as Shinrin-Yoku. As the host, Steve Curwood, describes it, forest bathing is a practice popular in Japan and China “in which practitioners spend meditative time breathing in nature.” The interviewee, Moshe Sherman, throws out several red flags typical of the evidence-challenged alternative medicine crowd, but he also makes some pretty specific health claims that he says are backed up by empirical evidence.

I’m going to argue that a lot of this is baloney. I want to be clear up front, though, that I’m not saying that walking in the woods and meditating in nature aren’t good for you. What I am saying is that the evidence that there’s something special about Shinrin-Yoku, something that provides benefits beyond those of exercise and relaxation, is lousy.

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One-stop shopping

I have an Etsy store. I opened it around the time of the Volvox wall art giveaway, and I’ll be the first to admit that it has a limited selection. Exclusive, you might say.

But I can promise you this: it is the world’s foremost source for micrographs of Volvox aureus printed on canvas. It is truly one-stop shopping if the only thing you need is micrographs of Volvox aureus printed on canvas (what else could you need?). If you are in the market for micrographs of Volvox aureus printed on canvas, you need look no further. Unless you can convince Piotr or Katrin to give up theirs, it is probably the only source for micrographs of Volvox aureus printed on canvas.

Volvox aureus

Volvox aureus by me

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“Sort of like a mass of crickets”

Cuban embassy

Image credit: ADALBERTO ROQUE/AFP/Getty Images.

As I have mentioned now and then over the last year and a half, the narrative that American embassy personnel in Cuba were subjected to “sonic attacks” is bullshit (Sonic stupidity; “It may seem the stuff of sci-fi novels”; More acoustic credulity; Cuba’s “magical sci-fi sound gun”; No means, no motive, and no suspect; More Cuban science fiction; Sonic weapons on Skeptoid; FBI dismisses sonic weapons in Cuba “attacks”; Asking the wrong questions: still no evidence of a sonic weapon):

There is no evidence that U.S. embassy officials in Cuba were subjected to any kind of attack. There are a bunch of reported symptoms that are not clearly related and mostly subjective. The symptoms are consistent with lots of other explanations; the only reason they’re being attributed to attacks is assertions by unnamed government officials. To my knowledge, none of these assertions are backed by evidence.

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