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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Evolution is religion; intelligent design is science

BizarroWorld

According to back-to-back posts on Evolution News and Views, evolution is religion, while intelligent design is science. In a badly argued post today, Cornelius Hunter says,

As I have explained many times, evolution is a religious theory…

Yesterday on the same platform, Steve Laufmann explained

…intelligent design is science, though not everyone knows it yet.

Well, he’s right about the second part.

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Heads I win; tails you lose redux

Image from www.twoheadedquarter.net.

Image from www.twoheadedquarter.net. Only $6.95!

I have previously complained that, for cdesign proponentsists,

…if multicellularity is really complicated, that’s evidence for intelligent design. But if multicellularity is really simple, that’s evidence for intelligent design.

Now here’s another example of this logic. Fellows of the Discovery Institute have been arguing for some time that the human and chimpanzee genomes differ by more than is usually reported, and that this (of course) supports intelligent design. [Read more…]

Please stop calling them pond scum

Gonium pectorale. Credit: Kansas State University.

Gonium pectorale. Credit: Kansas State University.

Yes, they live in ponds; no they don’t form any kind of scum. The press release from Kansas State on the Gonium genome paper, which is reprinted here, here, and here, is titled “Pond scum and the gene pool: One critical gene in green algae responsible for multicellular evolution, understanding of cancer origin.” Gonium forms planktonic colonies of (usually) 8, 16, or 32 cells that swim under their own power and exhibit phototaxis (they’ll swim toward a light source). They are not pond scum. ‘Algae’ and ‘pond scum’ are not synonyms, dig? Leaving aside the distinction between algae and cyanobacteria, calling Gonium pond scum is like saying pineapples are lemons (because both are fruits).

Also…cancer origin, really? You went there? The word ‘cancer’ does not appear in the paper except in the funding acknowledgements (Bradley Olson is partly funded by the KSU Johnson Cancer Center).

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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Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 3

Maureen O’Malley and Russell Powell say that the major transitions framework is in need of repair. They have a point, or rather several good points. I have looked at their criticisms of three different versions (the original framework as laid out in the book by John Maynard Smith and Eörs Szathmáry, Rick Michod’s ‘evolutionary transitions in individuality‘ framework, and Szathmáry’s revised ‘Major Transitions 2.0‘). But what is their proposed fix, and will it have the intended effect?

Figure 4 from O'Malley and Powell 2016. Two major aeons of evolution (modified from Falkowski 2006). ‘Gya’ stands for ‘billion years ago’; the date for the origin of photosynthesis may need to be pushed back (see Crowe et al. 2013).

Figure 4 from O’Malley and Powell 2016. Two major aeons of evolution (modified from Falkowski 2006). ‘Gya’ stands for ‘billion years ago’; the date for the origin of photosynthesis may need to be pushed back (see Crowe et al. 2013).

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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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One of the problems with a big tent

…is that the people in your tent only share some of your views. And one of the problems with having a blog is that it’s searchable, so that when you say ‘no one in my tent ever said x,’ it’s easy to show that it’s a lie.

Within the intelligent design tent, there are people like Michael Behe, who believe that species change over time and that they evolved from a common ancestor, differing from evolutionary biologists only in their insistence that some aspects of biology must have been designed:

I am not a creationist and have no reason to doubt common descent.

There are also people in the tent like Casey Luskin, Stephen C. Meyer, and Jonathon Wells who doubt, and spend a lot of their time attacking, common descent (see “Intelligent design’s relationship with common descent? It’s complicated.“).

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Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 2

One of the cool things about studying the so-called major transitions is that they are as interesting to philosophers of science as to biologists. So you really can’t help being exposed to the philosophy of science literature, and many (maybe most) biologists in the field cross the lines at least occasionally. I’ve been to both, and I’m here to tell you that philosophy conferences are more fun than biology conferences.

Last time, I briefly summarized the various forms of the major transitions framework and addressed one of O’Malley and Powell‘s criticisms, that the framework is progressivist. Now I’d like to look at their other two problems: lack of unity and missing events. By and large, I agree with these points, although there are some caveats I’d like to point out. Next time, I’ll consider their proposed solution, which I’m afraid I don’t find helpful.

Disunity is actually O’Malley and Powell’s first criticism, but it will be a bit more complicated than progressivism to address, and I was short on time on part 1. Essentially, they are arguing that the major transitions are not a natural kind, philosophese for groupings that belong together because of some fundamental commonality, as opposed to more arbitrary groupings whose members are only superficially similar. So what are the transitions? Here’s the list from the book:

Table 1.2 from Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution. Oxford University Press, Oxford.

Table 1.2 from Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution. Oxford University Press, Oxford.

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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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