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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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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Pleodorina starrii

32- and 64-celled colonies of Pleodorina starrii.

32- and 64-celled colonies of Pleodorina starrii. Not to scale. Creative Commons License
Pleodorina starrii by Matthew Herron is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

I spent a year in graduate school trying to cross male and female strains of the volvocine green alga Pleodorina californica. A year. I did some other stuff in that time, but I spent an awful lot of it trying to convince these algae to get busy. I threw everything I could think of at them: four different mating media, different temperatures, different lighting conditions…nothing worked. I never recovered a single viable zygote. I needed to cross them to generate some genetic variation for an ambitious artificial selection study, my ‘official’ dissertation project. Eventually, my advisor suggested I ask Hisayoshi Nozaki for advice.

There is little doubt that Dr. Nozaki is the world’s leading expert on volvocine biodiversity, having described about half of the known species (see for example New Volvox Species, Volvox ovalis, and African Volvox in Montana). He responded that the strains of Pleodorina californica I had been failing to breed had been collected many years ago and had probably lost the ability to reproduce sexually (a problem I mentioned in Why don’t we revise volvocine taxonomy?). I had been spinning my wheels, never realizing that I had no hope of success. I should have contacted Dr. Nozaki about eleven months earlier.

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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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Volvox meeting review online early

Fig. 1 from Herron 2016. Examples of volvocine species. (A) Chlamydomonas reinhardtii, (B) Gonium pectorale, (C) Astrephomene gubernaculiferum, (D) Pan- dorina morum, (E) Volvulina compacta, (F) Platydorina caudata, (G) Yamagishiella unicocca, (H) Colemanosphaera charkowiensis, (I) Eudorina elegans, (J) Pleodorina starrii, (K) Volvox barberi, (L) Volvox ovalis, (M) Volvox gigas, (N) Volvox aureus, (O) Volvox carteri. Figure Credit for A and B: Deborah Shelton.

Fig. 1 from Herron 2016. Examples of volvocine species. (A) Chlamydomonas reinhardtii, (B) Gonium pectorale, (C) Astrephomene gubernaculiferum, (D) Pandorina morum, (E) Volvulina compacta, (F) Platydorina caudata, (G) Yamagishiella unicocca, (H) Colemanosphaera charkowiensis, (I) Eudorina elegans, (J) Pleodorina starrii, (K) Volvox barberi, (L) Volvox ovalis, (M) Volvox gigas, (N) Volvox aureus, (O) Volvox carteri. Figure Credit for A and B: Deborah Shelton.

Pretty much what the title says: the meeting review from Volvox 2015 is online early at Molecular Ecology. That only took six months! This is the final, published version. Thanks for a great meeting, and thanks to everyone who read earlier drafts!

Volvox in Highlights Magazine

Highlights_screenshot

This is so cool! The March issue of Highlights Magazine (“Fun with a purpose”) includes a full page on Volvox. Highlights is aimed at kids 6-12 and publishes both print and digital editions:

In every 40-page issue, kids explore new topics, investigate cool subjects and find out about the world. Highlights magazine for kids is filled with stories, games, puzzles, riddles, science experiments, craft projects and interactive entertainment!

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Moving without limbs! Linnaeus on Volvox

 

Linnaeus - 1758

In ancient times, when dusky seaside sparrows still roamed the Earth, I took two years of high school Latin. My Latin name was Matteus (we were all required to call each other and Mrs. Knowles by our Latin names); my Latin motto was “carpe diem.” That’s about how much I remember. Thankfully, in these modern times, we have Google Translate*. If you remember more Latin than I do, please feel free to correct my translations in the comments.

Linnaeus gave Van Leeuwehoek’s “great round particles” the name Volvox in his Systema Naturae. Linnaeus lists two species of “Volvox“, V. globator and V. chaos. “Volvox chaos” is an amoeba now known as Chaos sp. (though there is some confusion about its exact identity). Although AlgaeBase lists V. chaos as a valid taxon, Leidy (1879, pp. 30-35) reviews the synonymy of Chaos, and it is clearly an amoeba, not an alga.

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