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:

 

Salutations! Matt did a fantastic job getting the ball rolling with his first post on the ENV response to the Gonium genome paper, and he was kind enough to let me join in on the fun for part 2. Thanks Matt!

As a reminder, creatidesignists don’t like scientists studying the evolution of multicellularity, as demonstrated by the fact they respond to nearly every high impact paper published. In my mind, there are two major responses to the ENV article that remain, the subject of gene duplications and the concept of model organisms. There’s also a minor point I think should be made so I’ll start with that.

There are a LOT of relatively minor errors in the ENV response:

  1. “This from researchers at the University of Witwatersrand”- only 1 of 22 authors is from the University of Witwatersrand. This is obvious given the paragraph of affiliations on the first page.
  2. “Well, in the original paper in Nature Communications, there are three different types of algae discussed”- We actually went to great lengths to include eight other green algae in our analyses, which was important for our analyses and conclusions. See every panel of Figure 2.
  3. They repeatedly confuse the plural “algae” with singular “alga”.
  4. Gonium pectorale, a colonial algae [sic] where each cell is identical;” Matt already did a great job correcting this.
  5. Chlamydomonas, a non-colonial algae [sic]” Again, Matt already did a great job correcting this.
  6. Volvox, another type of colonial algae [sic] that, however, does have differentiated cells”- By convention only undifferentiated species are referred to as ‘colonial’.
  7. “They put the Gonium pectorale versions of the genes”- We only transformed a single gene, RB, not multiple genes.
  8. “They know these forms of algae behave differently, so they’re comparing the genetic bases for that behavior”- News to me! The word ‘behavior’ never appears in our paper, we’re studying the genetic basis for morphology.
  9. “They haven’t determined…whether there are multimutation features involved”- What the heck is a ‘multimutation feature’??

I know these are minor and esoteric, but in a single page of writing, this is a lot! Did they even read the paper? Are they familiar at all with the field? This is the care and diligence they bring to the discussion? If they can’t get the easy, simple details right, what makes you think they’d get the difficult, complex concepts right?

On to the major responses. First, gene duplication. Some of the important differences among the Chlamydomonas, Gonium, and Volvox genomes are gene duplications. These include expansions of cyclin D genes, transcription factors that regulate cellular differentiation in Volvox, and gene families called pherophorins and metalloproteases, which are related to the extracellular matrix of Volvox. But the creatidesignists dismiss this quite easily:

“They merely assert that these genes evolved.”

Au contraire! We show these genes are in tandem arrays (up to 10 pherophorin genes in a row along the chromosome), we show these genes are phylogenetically very closely related (some six different phylogenies), and we also know from previous research that the volvocine algae have high rates of gene duplication. Those first two points are precisely predicted from a known mechanism of gene duplication, unequal crossing over, where imperfect recombination during meiosis results in gene duplication.

The creatidesignists are confusing “assert” and “give convincing evidence”.

The second major point- the concept of model organisms. The ENV article effluent betrayed a profound ignorance of the concept of model organisms and model systems with this gem:

“Note that the authors acknowledge multicellularity has evolved “numerous times in all domains of life.” So one doubts that this example explains how it occurred in other cases.”

A major reason that we study the volvocine green algae is because they allow insight into other multicellular groups, like plants and animals. These groups share important properties relevant to the evolution of multicellularity, such as cell walls, cellular differentiation, and flagellation. For example, in the volvocine algae, the cellular machinery (basal bodies) that controls mitotic separation of chromosomes, also provides an anchor for flagella. This creates a tradeoff- a cell can either beat flagella or undergo mitosis/meiosis. The same cellular machinery, the same tradeoff, and the same lessons, exists in animals (Marshall 2008).

There are characteristics unique to the volvocine algae. The distance between cells likely prevents direct cell-cell communication or signaling. But this is a good thing. Having a variety of different multicellular forms allows us to learn from both the similarities and the differences.

There are also practical concerns for using the volvocine algae as a model system- they evolved more recently than plants or animals, meaning they are more similar to their unicellular relatives than plants or animals are to theirs. This allows easier genomic comparison and easier morphological comparison (because a cell from Volvox looks more like a Chlamydomonas cell than a human cell looks like a choanoflagellate cell). These practical concerns, coupled with the similarities to plants and animals, make the volvocine green algae a fantastic model system.

There’s a delightful irony when the creatidesignists say “So one doubts that this example explains how it occurred in other cases” right before quoting our discussion about RB in plants and animals.

“In plants and animals, RB proteins are important for regulating both cell proliferation and differentiation”

We’ve shown similar expansions of cyclin D genes (which regulate RB) in volvocine algae, plants, and animals. We’ve demonstrated a causal link between a cell cycle regulator, RB, shared across the eukaryotic tree of life and the formation of undifferentiated groups. I think this strengthens the volvocine algae as a model system for the evolution of multicellularity, illuminating how multicellularity evolved in other cases.

 

Stable Links:

Marshall WF (2008), Chapter 1 Basal Bodies: Platforms for Building Cilia, Current Topics in Developmental Biology, Academic Press, Volume 85.

Comments

  1. Johnny Vector says

    Cdesign Proponentsists:

    So one doubts that this example explains how it occurred in other cases.

    As they pretend not to notice that when your argument consists of “it’s inconceivable that evolution could have resulted in X,” it only takes one counterexample to falsify your claim.

    “Sure, this one might have evolved, but how do you know God didn’t design some other multicellular organism? So there.”

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