Paywalls revisited

Say you think I’m full of it. Or Larry Moran is. Or ScienceNews, or Scientific American, or PhysOrg. One of us has written about a peer-reviewed paper, and you think maybe we’ve misrepresented it, or cherry-picked the bits we like, or you just want to read a more complete story. There’s good reason to be skeptical: news organizations (and bloggers) misunderstand, misrepresent, or exaggerate scientific studies all the time. But the article is behind a paywall, and you don’t want to have to shell out serious money every time you have your doubts. So you just have to take our word for it, right? Not usually.

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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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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!

Changing into my old genes: Betül Kaçar’s molecular paleontology

Tape of life logo

Betül Kaçar has posted another preprint to bioRxiv describing her work combining molecular paleontology with experimental evolution. I’ve written about Dr. Kaçar’s research, and the Discovery Institute’s bizarre interpretations, before, and I won’t be surprised if the cdesign proponentsists feel compelled to respond again.

The new preprint describes experimental evolution in E. coli bacteria genetically engineered to express an ancient protein in place of its modern counterpart. The gene encoding the protein, Elongation Factor Tu (EF-Tu), exists in two copies in the wild-type E. coli genome. Dr. Kaçar’s team deleted one copy and replaced the other with a gene sequence inferred to be similar to that in E. coli‘s ancestor from 700 million years ago.

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Levels of selection in biofilms: Ellen Clarke on individuality

Pseudomonas biofilm. From Spiers et al. 2013.

Pseudomonas biofilm. From Spiers et al. 2013.

The question of what constitutes a biological individual is intimately entangled with questions about levels of selection. Many authors implicitly or explicitly treat individuals as units of evolution or some variation on this theme. A recent appreciation for the complexity of bacterial biofilms has led to comparisons with multicellular organisms. A recent paper by Ellen Clarke bucks this trend by claiming that multispecies biofilms are not evolutionary individuals.

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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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Volvox 2015 meeting review available online

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.

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. A and B by Deborah Shelton.

The meeting review for the Third International Volvox Conference is now available online at Molecular Ecology (doi: 10.1111/mec.13551). The editors warned me ahead of time that the challenge for this paper would be to make it of broad interest to the readership of Molecular Ecology, so there is a lot of background information that will be old news to members of the Volvox community.

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Karen Kovaka on biological individuality

At the Philosophy of Science Association meeting in Chicago, I attended an interesting talk by Karen Kovaka, “Biological Individuality and Scientific Practice” (the abstract of her talk is here). Now the paper arising from that talk is out in the journal Philosophy of Science. It argues that biologists do not need to resolve the question of what constitutes an individual in order to do good empirical work, with which I agree. She contrasts two views of the relationship between individuality and scientific practice, the “quality dependence” account and the “content sensitivity” account:

Quality dependence: the quality of empirical work in biology depends in part on the resolution of the debate about biological individuality…

Content sensitivity: Biologists’ understanding of biological processes is sensitive to the individuals they take to be participants in those processes.

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New Volvox species

Hisayoshi Nozaki and colleagues have done it again: in a new PLoS One article, they have described yet another new species of Volvox, V. reticuliferus (see also “Volvox 2015: taxonomy, phylogeny, & ecology“):

Figure 1A from Nozaki et al. 2015: Surface view of asexual Volvox reticuliferus spheroids.

Figure 1A from Nozaki et al. 2015: Surface view of asexual Volvox reticuliferus spheroids.

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Hexadecaflagellates!

Kirsty Wan and Ray Goldstein have posted a new paper to arXiv*: “Coordinated Beating of Algal Flagella is Mediated by Basal Coupling.” The paper examines in unprecedented detail the mechanics of intracellular flagellar coordination. That’s cool and all, but first: hexadecaflagellates!

Wan & Goldstein compared algal cells with 2, 4, 8, and, yes, 16 flagella. I never knew there was such a thing. Pyramimonas cyrtoptera has 16, and its relative P. octopus has…well, you can probably guess.

Fig. 7 from Wan and Goldstein 2015: Pyramimonas cyrtoptera.

Fig. 7 from Wan & Goldstein 2015: Pyramimonas cyrtoptera, with hella flagella.

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