A cautionary tale on reading phylogenetic trees

I have written before about the perils of naive interpretations of phylogenetic trees (“Extant taxa cannot be basal“). Others, notably Krell & Cranston and Crisp & Cook, have pointed out that this is not just a language issue; such misreadings can cause substantive problems in the way evolutionary history is understood.

A new paper in PLoS ONE, “A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species,” contains several instructive examples. PLoS ONE is open access, so you can read the original paper without an institutional subscription. A tweet by Frederik Leliaert got this paper on my radar, and it piqued my interest because of the startling observation that the inferred phylogeny shows Chlamydomonas as sister to all other eukaryotes.

It made me frown, too.

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Mechanics of Volvox inversion

Variation is everywhere in biology. Structural variation is present at molecular, cellular, organismal, and population levels, and functional variation occurs in processes from metabolism to development to behavior. In spite of this, we often describe biology in typological terms, and this is often a source of confusion.

Some variation is crucial; for example, evolution is dependent on genetic variation, and behavioral variation within ant and bee colonies ensures that all the necessary jobs get done. Much variation, though, is simply biological noise, an unavoidable consequence of the mostly analogue nature of living systems. In extreme cases, variation of this sort can complicate and even derail development, but in general development is remarkably robust. A variety of regulatory mechanisms prevent small amounts of variation early in development from being amplified into large variations in adults.

Pierre Haas and colleagues have posted a preprint to arXiv describing variation in the developmental process of inversion in Volvox globator. Facultatively sexual organisms such as Volvox are great for studying non-genetic sources of variation, because it’s pretty simple to produce millions of genetically identical individuals. When they are raised in identical conditions, variation due to environmental differences is minimized, and most of the observed variation is stochastic.

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Another step toward understanding sex determination in Volvox

Volvox and its relatives are a great model system for understanding the evolution of multicellularity. Their simplicity (relative to most other multicellular groups) and the variety of ‘intermediate’ species (‘intermediate’ in terms of size and complexity) make them especially suitable for comparative studies of their morphology, development, genetics, genomics, and so on. David Kirk’s book on the topic thoroughly reviews the work done up through the late ’90s, and advances since then have only increased the pace of discovery.

But in the last ten years or so, I would argue that the volvocine algae have emerged as a leading model system for an entirely different set of questions related to the evolution of the sexes. Males and females are defined by the gametes they produce, and the sexes came into existence when their gametes diverged into two different types. The existence of different male and female gametes (sperm and eggs, in most cases) is called anisogamy, and the ancestral condition of similar gametes is isogamy.

In 2006, Hisayoshi Nozaki and colleagues reported that volvocine males evolved from the minus (isogamous) mating type. To the best of my knowledge, this is the only group for which we know this. Since then, more clues have been forthcoming, and these were competently reviewed last year by Takashi Hamaji and colleagues. A new paper in PLoS ONE, by Kayoko Yamamoto and colleagues, adds another piece to the puzzle.

Figure S2 from Yamamoto et al. 2017. Light microscopic images of Volvox africanus (homothallic, monoecious with males type) and V. reticuliferus (heterothallic, dioecious type). Scale bars = 50 μm. sp: sperm packet, e: egg. A-C. V. africanus strain 2013-0703-VO4. A. Asexual spheroid. B. Monoecious spheroid. C. Male spheroid. D, E. V. reticuliferus. D. Male spheroid in male strain VO123-F1-7. E. Female spheroid in female strain VO123-F1-6.

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A confused mess, part 1

I follow Uncommon Descent to keep up with what the cdesign proponentsists are up to, even though I’ve been banned from commentingUncommon Descent pushes out about three times as many articles as Evolution News & Views, and it’s clear that less than a third as much thought goes into each one. Worse, the articles’ authorship is rarely identified, robbing me of my second favorite sport after fly fishing, pointing out creationists’ self-contradictions. For both of these reasons, I don’t comment on their posts nearly as often. But if you read this blog at all, you must know that I can’t pass on a video that 1) claims to provide evidence against evolution and 2) has Volvox in it.

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Another take on volvocine individuality

Dinah Davison & Erik Hanschen

Dinah Davison and Erik Hanschen.

A couple of weeks ago, I indulged in a little shameless self-promotion, writing about my new chapter on volvocine individuality in Biological Individuality, Integrating Scientific, Philosophical, and Historical Perspectives. Now two graduate students in the Michod lab at the University of Arizona, Erik Hanschen and Dinah Davison, have published their own take on volvocine individuality in Philosophy, Theory, and Practice in Biology (“Evolution of individuality: a case study in the volvocine green algae“). The article is open-access, and Hanschen and Davison are listed as equal contributors.

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Non-model model organisms

Jim Umen, the lead organizer of the upcoming Volvox meeting, has written a section for a new paper in BMC Biology, “Non-model model organisms.” Like all of the BMC journals, BMC Biology is open access, so you can check out the original.

The article surveys organisms that, while not among the traditional model systems, have been developed as model systems for studying particular biological questions. The paper has an unusual format, with a discrete section devoted to each species, each written by one or two of the authors. Aside from Volvox, there are sections on diatoms, the ciliates Stentor and Oxytricha, the amoeba Naeglaria, fission yeast, the filamentous fungus Ashbya, the moss Physcomitrella, the cnidarian Nematostella, tardigrades, axolotls, killifish, R bodies (a bacterial toxin delivery system), and cerebral organoids (a kind of lab-grown micro-brain).

Dr. Umen presents Volvox and its relatives as a model system for understand the evolution of traits related to the evolution of multicellularity:

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Cells, colonies, and clones: individuality in the volvocine algae

Biological Individuality

As I mentioned previously, I have a chapter in the newly published book Biological Individuality, Integrating Scientific, Philosophical, and Historical Perspectives. The chapter was actually written nearly five years ago, but things move more slowly in the philosophy world than that of biology. Finally, though, both the print and electronic versions are now available; here is the electronic version of my chapter. The book currently has no reviews on Amazon, so if you want to give it a read, yours could be the first. If you’re interested in current and historical views on individuality, there is a lot of good stuff in here, including contributions by Scott Lidgard & Lynn Nyhart, Beckett Sterner, Andrew Reynolds, Snait Gissis, Olivier Rieppel, Michael Osborne, Hannah Landecker, Ingo Brigandt, James Elwick, Scott Gilbert, and Alan Love & Ingo Brigandt.

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