A series of fortunate events

Salomé and Merchant 2019 Fig. 1

Figure 1 from Salomé and Merchant 2019. Taxonomic Basis of Chlamydomonas and Volvox. Ehrenberg’s drawings of Chlamydomonas and Volvox cells, published in 1838. Cells that belong to the same species are indicated by Roman numerals in the right panel. I, Gonium pectorale; II, Gonium punctatum; III, Gonium tranquillum; IV, Gonium hyalinum; V, Gonium glaucum; VI, Eudorina elegans; VII, Syncrypta volvox; VIII, Sphaerosira volvox; IX, Synura uvella; X, Chlamidomonas pulvisculus; XI, Uroglena volvox. The species was identified as Chlamidomonas pulvisculus but renamed Chlamydomonas reinhardtii in 1888.

In a new(-ish) article in The Plant Cell, Patrice Salomé and Sabeeha Merchant review the history and utility of the green alga Chlamydomonas reinhardtii as a model organism. The article discusses the advantages of Chlamy as a model organism, the scientific questions it has been used to explore, the history of Chlamy research, the characteristics of the species, the existing resources and databases, and genetic and genomic techniques. It’s a good introduction to Chlamy research in a more easily-digestible form than the massive, three-volume Chlamydomonas Sourcebook.

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Upcoming talks, and some system maintenance

Chlamydomonas colonies from the predation experiment.

Chlamydomonas colonies from the predation experiment.

I’ll be giving a couple of talks on experimental evolution of multicellularity in the next couple of weeks:

  1. University of Georgia Department of Cellular Biology, Tuesday, September 11, 11:00 a.m. in Biological Sciences 404A
  2. Donald Danforth Plant Science Center, Friday, September 20, time and place TBD

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Debunked by the Institute for Creation Research

Folks, it’s been fun. I feel like I had a pretty good run as a scientist. I met some amazing people, went to beautiful places, and learned things I never would have imagined (Hodgkinia, WTF?!). With all my frustrations and failures, I’ve never once regretted going back to school and becoming a biologist. But now I need to close the door on all of that and find a new way to make a living.

See, the main project I’ve been working on for the last six years, the one that was supported by a NASA postdoctoral fellowship, and that just came out in Scientific Reports, has been debunked:

ICR screenshot [Read more…]

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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Convergence part 6: the deepest of deep homologies

You are more closely related to a mushroom than a kelp is to a plant. It’s strange to think about, but it’s true. Kelps seem very plant-like, with their root-like holdfasts, stalk-like stipes, and leaf-like blades. But kelps are brown algae, part of the stramenopile (or heterokont) lineage of eukaryotes, which are very distant from the land plants and their green algal relatives, all of which are within the archaeplastida (the direct descendants of the primary origin of chloroplasts). Mushrooms (fungi) and humans (animals), on the other hand, are both opisthokonts, practically cousins at the scale we’re talking about.

Pawlowski 2013 Fig. 1

Figure 1 from Pawlowski 2013. Deep phylogeny of eukaryotes showing the position of small eukaryotic lineages that branch outside the seven supergroups (modified after Burki et al. 2009; drawings S Chraiti). You are represented by a fish, which at this scale you might as well be.

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Flagellar synchronization in Chlamydomonas

The physics is way beyond me, but a new paper by Gary Klindt and colleagues in New Journal of Physics uses Chlamydomonas as a model for flagellar synchronization:

We present a theory of flagellar synchronization in the green alga Chlamydomonas, using full treatment of flagellar hydrodynamics and measured beat patterns. We find that two recently proposed synchronization mechanisms, flagellar waveform compliance and basal coupling, stabilize anti-phase synchronization if operative in isolation. Their nonlinear superposition, however, can stabilize in-phase synchronization for suitable parameter choices, matching experimental observations.

Klindt et al. Fig. 1

Figure 1 from Klindt et al. 2017. In-phase and anti-phase synchronization. (a) In-phase synchronization at high synchronization strength, corresponding to “breast-stroke swimming” Chlamydomonas. (b) For low synchronization strength, anti-phase synchronization is stable, corresponding to a “free-style” gait.

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