New position at Georgia Tech

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Part of the reason posts at Fierce Roller have been so sparse lately is that I’ve been busy moving across the country. I’m now a Senior Research Scientist in the School of Biology at Georgia Tech. I’ll be running a small lab, with two (soon three) postdocs and a very talented grad student.

I spent exactly one day on campus before I left for the ASM Experimental Microbial Evolution meeting, on which I managed to meet with the grad student and one postdoc and to get hooked up to the campus wifi. I have not yet attended new employee orientation or been assigned an employee ID number, so the degree to which I’m actually employed at this moment is a bit murky. Hopefully I’ll get this all sorted next week.

Graduate student position in the Nedelcu lab

If you’re a fan of Volvox and the volvocine algae and have recently received an undergraduate degree in biology or a related field, now’s your chance to get serious about studying them. Aurora Nedelcu is looking for a graduate student to join her lab at the University of New Brunswick. Professor Nedelcu is a major player in the Volvox community, having published foundational papers on diverse aspects of volvocine biology and organized the first two international Volvox meetings. This is a great opportunity to join a vibrant and growing research community:

A graduate student position is available in the laboratory of Aurora Nedelcu, in the Department of Biology at the University of New Brunswick, Fredericton, CANADA. Research in our laboratory is directed towards understanding general, fundamental issues in evolution – such as the evolution of multicellularity, development, cell differentiation, sex, programmed cell death, altruism.  Our research is rooted in the framework of transitions in individuality and evolution of complexity (at a conceptual level), and of cellular responses to stress (at a more mechanistic level).  The experimental model-system we are currently using is the green algal group, Volvocales (see our Volvocales Information Project; http://www.unbf.ca/vip). Highly motivated students with interests in either theoretical/genomics or experimental/molecular approaches, and previous research experience are encouraged to apply. Interested applicants should e-mail a CV, summary of research experience and interests, unofficial transcripts, and contact information for three referees to [email protected].

Applicants should meet the minimum requirements for acceptance in the Biology Department Graduate Program (see http://www2.unb.ca/biology/Degree_Info/Graduate.html).

The evolution of undifferentiated multicellularity: the Gonium genome

Blogging took a backseat to the wedding of two dear friends two weekends ago and to morel hunting last weekend, so I’m only now getting around to a post that should have been written weeks ago (I promised on April 22 that it would be out the following week). Last month, Erik Hanschen and colleagues published the Gonium pectorale genome, filling in some crucial bits of the transition to multicellular life in the volvocine algae. This was a big project, taking several years and involving over 20 authors from over a dozen institutions. The final paper is open access in Nature Communications.

I did post an effort to explain some aspects of the paper to the cdesign proponentsists at Evolution News and Views, who, by their own admission, failed to understand it (“After reading this paper, we’re none the wiser.”). I also complained of the science media’s tendency to refer to all algae as ‘pond scum.’ The lead author of the genome paper kindly followed up with a guest post addressing some of ENV‘s other misunderstandings, such as the purpose of model organisms in biology and the difference between ‘assertion’ and ‘evidence’. But now it’s time to dig into what the genome paper actually says.

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Heads I win; tails you lose: Evolution News & Views on Gonium, part 2: Model systems and gene duplication

Figure 2 from Hanschen et al. 2016. (a) Predicted number of genes in each phylostratum (PS1–PS9) for Chlamydomonas, Gonium and Volvox. (b) Heatmap of transcription factor abundance for all green algae. Significant over- (+) and under-representation (−) in colonial/multicellular lineages (Gonium and Volvox) is denoted (G test of independence, α=0.05). Rows are clustered (left), an accepted phylogeny is depicted (top). (c) Phylogenetic analysis of gene family evolution. Bars to the left and right of the vertical axis denote the lost and gained gene families respectively, relative to its parental node. (d) Venn diagram of the species distribution of Pfam A domains unique to the volvocine algae.

Figure 2 from Hanschen et al. 2016. (a) Predicted number of genes in each phylostratum (PS1–PS9) for Chlamydomonas, Gonium and Volvox. (b) Heatmap of transcription factor abundance for all green algae. Significant over- (+) and under-representation (−) in colonial/multicellular lineages (Gonium and Volvox) is denoted (G test of independence, α=0.05). Rows are clustered (left), an accepted phylogeny is depicted (top). (c) Phylogenetic analysis of gene family evolution. Bars to the left and right of the vertical axis denote the lost and gained gene families respectively, relative to its parental node. (d) Venn diagram of the species distribution of Pfam A domains unique to the volvocine algae.

Erik Hanschen, the lead author on the Gonium genome paper, is also an old friend of mine from when we were both in Michael Doebeli’s lab at the University of British Columbia. He kindly agreed to write a guest post responding to Evolution News and Views‘ misunderstandings of his paper. Everything below the fold was written by Erik:

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Heads I win; tails you lose: Evolution News & Views on Gonium, part 1

Figure 6 from Hanschen et al. 2016. Multicellularity hinges on the evolution of cell cycle regulation in a multicellular context with subsequent evolution of cellular differentiation (here, cell size-based) and increased body size.

Figure 6 from Hanschen et al. 2016. Multicellularity hinges on the evolution of cell cycle regulation in a multicellular context with subsequent evolution of cellular differentiation (here, cell size-based) and increased body size.

Remember how I said they’re prolific? Before I’ve even had a chance to write up my thoughts on the Gonium genome paper, Evolution News & Views has already published theirs. The story has also been picked up by the Washington Post, New Historian, GenNews, and ScienceDaily (that last one looks like just a reprint of the press release from University of the Witwatersrand). By the way, the genome paper is open access, so you don’t need a subscription to see it for yourself.

We already know that cdesign proponentsists are not fans of research into the evolution of multicellularity, and that they have trouble understanding it. In an unsigned article on the Gonium genome at ENV, they admit that

After reading this paper, we’re none the wiser.

That’s too bad. I’m here to help.

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Gonium genome published

Figure 1 from Hanschen et al. 2016. (a) Evolution of cell cycle control (C), expanded ECM (E) and somatic cells (S) are denoted. (b) Micrographs of Chlamydomonas (green; scale bar, 10 μm), Gonium (blue; scale bar, 10 μm) and Volvox (black; scale bar, 25 μm) show morphological differences.

Figure 1 from Hanschen et al. 2016. (a) Evolution of cell cycle control (C), expanded ECM (E) and somatic cells (S) are denoted. (b) Micrographs of Chlamydomonas (green; scale bar, 10 μm), Gonium (blue; scale bar, 10 μm) and Volvox (black; scale bar, 25 μm) show morphological differences.

I haven’t read it yet and won’t have time today, but the Gonium pectorale genome paper just came out in Nature Communications! Erik Hanschen is the lead author, and the article is open access. I previously reported on Erik’s talk at Volvox 2015:

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Origins of the sexes: Takashi Hamaji on mating type determination

The evolution of sex is one of the big outstanding problems in evolutionary biology. The origin of sex is one of Maynard Smith and Szathmáry’s “Major Transitions,” on which I’m currently teaching a course here at the University of Montana. Our discussion of sex luckily coincided with the visit of the grad-invited Distinguished Speaker, Sally Otto, an important theorist on this topic (among others). Dr. Otto generously agreed to join us for the discussion, which turned out to be one of the best we’ve had.

A related problem to the origin of sex is the origin of males and females. Sexual reproduction doesn’t always involve males and females: lots of species that don’t even have males and females have sex. There are lots of traits that we associate with males and females — fancy plumage, differences in body size and type of genitalia, presence and absence of exaggerated weapons — but what actually defines males and females is differences in gamete size. Animals, plants, and other organisms with males and females are oogamous: males have small, swimming sperm, and females have large, immotile eggs. But lots of single-celled eukaryotes have only one size of gamete. We call these isogamous (‘equal gametes’).

Some volvocine algae are isogamous (such as Chlamydomonas), some are oogamous (such as Volvox), and some (such as Pleodorina) are anisogamous (‘unequal gametes’), meaning that the gametes come in two sizes but both can swim. In spite of not having sexes per se, Chlamydomonas, like a lot of isogamous organisms, comes in two ‘mating types’, which are arbitrarily called ‘plus’ and ‘minus.’ The mating types are self-incompatible, in other words plus can only mate with minus and vice versa.

All this variation in mating systems makes the volvocine algae a great model system for understanding the evolution of sex and the sexes (see ‘Volvox 2015: all about sex‘). We know from previous work that males evolved from the minus mating type and females from the plus in this lineage. But males and females have evolved from isogamous ancestors many times, and to my knowledge we don’t know which came from which for any other group.

Takashi Hamaji and colleagues have just published an analysis of the genomic region that determines mating type in Gonium pectorale, an isogamous alga more closely related to Volvox than to Chlamydomonas.

Figure 1 from Hamaji et al 2016. A schematic diagram for phylogenetic relationships of selected volvocine species based on Nozaki et al. (2000); Herron and Michod (2008). The top row illustrates gamete type and structure. Tubular mating structures in isogamous gametes are indicated with red bars at the flagellar base. The possession of a MID gene is shown next to the minus mating type or male gametes. The lower row of cartoons depicts vegetative morphology (not to scale) for the indicated species.

Figure 1 from Hamaji et al 2016. A schematic diagram for phylogenetic relationships of selected volvocine species based on Nozaki et al. (2000); Herron and Michod (2008). The top row illustrates gamete type and structure. Tubular mating structures in isogamous gametes are indicated with red bars at the flagellar base. The possession of a MID gene is shown next to the minus mating type or male gametes. The lower row of cartoons depicts vegetative morphology (not to scale) for the indicated species.

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Controlling contamination in Chlamydomonas cultures

Figure 1 from Wang et al. 2016.  Effects of bactericide/fungicide cocktails on the removal of microbial contaminants from Chlamydomonas reinhardtii cultures.

Figure 1 from Wang et al. 2016. Effects of bactericide/fungicide cocktails on the removal of microbial contaminants from Chlamydomonas reinhardtii cultures. (A) Control plate. (B) Plate with the One-shot Solution cocktail composed of ampicillin, cefotaxime, and carbendazim. (C) Plate with axoxystrobin and nalidixic acid. (D) Plate with tebuconazole and nalidixic acid. 1: uncontaminated cultures; 2–4: contaminated cultures containing fungi and bacteria.

A new paper in BioTechniques describes an improved antibiotic cocktail for controlling bacterial and fungal contamination of Chlamydomonas cultures. This is a problem that has cost our lab many hours, especially when using media that include acetate.

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