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!

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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The flip side of the Galileo Gambit: Denyse O’Leary on multicellularity

Figure 7 from Anderson et al. 2016. Evolution of GKPID’s new function by unveiling a latent protein-binding site. (A) The binding surface for Pins in GKPIDs is derived from the GMP-binding surface of gk enzymes. Homology models of Anc-gkdup (left) and Anc-GK1PID (right) are shown as white surface, with all side chains that contact either GMP or Pins as yellow sticks. Pink sticks show GMP; green ribbon shows Pins backbone, with the side chains of all Pins residues that contact the GK protein shown as sticks. The phosphate group on GMP and on Pins residue 436 are shown as orange and red sticks. Black dotted lines, protein-ligand hydrogen bonds. In the AncGK1PID structure , substitutions at sites in the binding interface are shaded red, including key substitution s36P. The binding modes of extant gk enzymes and GKPIDs are similar and support the same conclusions (see Figure 7—figure supplement 1). (B) The structure of the hinge and GMP/Pins-binding lobes is conserved between the Pins-bound GKPID (blue, rat Dlg, 3UAT), the apo-gk enzyme (brown, S. cerevisiae guanylate kinase 1EX6), and the apo-gk-s36P mutant (gray, 4F4J), all in the open conformation.

Figure 7 from Anderson et al. 2016. Evolution of GKPID’s new function by unveiling a latent protein-binding site. (A) The binding surface for Pins in GKPIDs is derived from the GMP-binding surface of gk enzymes. Homology models of Anc-gkdup (left) and Anc-GK1PID (right) are shown as white surface, with all side chains that contact either GMP or Pins as yellow sticks. In the AncGK1PID structure , substitutions at sites in the binding interface are shaded red, including key substitution s36P. (B) The structure of the hinge and GMP/Pins-binding lobes is conserved between the Pins-bound GKPID (blue, rat Dlg, 3UAT), the apo-gk enzyme (brown, S. cerevisiae guanylate kinase 1EX6), and the apo-gk-s36P mutant (gray, 4F4J), all in the open conformation.

Cdesign proponentsists really don’t seem to like research on the evolution of multicellularity. Pretty much any time real scientists learn something new about the origins of multicellularity, writers on intelligent design blogs Evolution News & Views and Uncommon Descent feel compelled to tell us why it’s wrong (for example, here, here, here, here, here, here, here, here, here, here, here, here, and here).

So I shouldn’t be surprised that Denyse O’Leary has weighed in on the latest work out of Ken Prehoda’s lab, in which Prehoda and colleagues identified a mutation crucial for forming and maintaining tissues in animals. Worse, from O’Leary’s point of view, the article describes the evolution of a new protein function, which is anathema to intelligent design thinkers. To say this post is badly argued is overly generous; it’s absolutely devoid of any substantive argument.

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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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Volvox 2015: taxonomy, phylogeny & ecology

Volvox africanus

Volvox africanus (from Herron et al. 2010)

The worst-kept secret among Volvox researchers is that the current volvocine taxonomy is a train wreck. Within the largest family, the Volvocaceae, five nominal genera are polyphyletic (Pandorina, Volvulina, Eudorina, Pleodorina, and Volvox). Of the remaining three, two are monotypic (Platydorina and Yamagishiella). Only the newly described Colemanosphaera is monophyletic with more than one species. The extent of the problem was suspected long before it was confirmed by molecular phylogenetics, and ad hoc attempts to deal with it have led to the existence of such taxonomic abominations as ‘sections,’ ‘formas,’ and ‘syngens.’ An overhaul is called for, but it is complicated by the aforementioned loss of type cultures.

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Pathways to pluralism: Beckett Sterner on biological individuality, part 2

Aphids on dandelion

Aphids on dandelion. Public domain image from Wikimedia Commons.

Previously, I introduced Beckett Sterner’s new paper comparing and critically evaluating the views of Ellen Clarke and Peter Godfrey-Smith on biological individuality. For Clarke, individuality is recognized by the presence of ‘individuating mechanisms’: traits that increase the capacity for among-unit selection or decrease the capacity for within-unit selection. Godfrey-Smith recognizes different kinds of individuals, but at a minimum, populations of individuals must have Lewontin’s criteria of phenotypic variation, differential fitness, and heritability of fitness, i.e. be capable of adaptive change.

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Why don’t we revise volvocine taxonomy?

Volvocine taxonomy is in a sorry state. Most nominal genera, and some nominal species, are almost certainly polyphyletic. More than once, I’ve been asked during a talk, “Why is Volvox scattered all over the tree?”

JPhycol2010Fig2a

Fig. 2A from Herron et al. 2010. The traits characteristic of the genus Volvox—asexual forms with >500 cells, only a few of which are reproductive, and oogamy in sexual reproduction—have arisen at least three times independently: once in the section Volvox (represented by V. globator, V. barberi, and V. rousseletii), once in V. gigas, and once or possibly twice in the remaining Volvox species. Branch shading indicates maximum-parsimony reconstruction (white = absent, black = present, dashed = ambiguous). Pie charts indicate Bayesian posterior probabilities at selected nodes. Numbers to the left of cladograms indicate log-Bayes factors at selected nodes: positive = support for trait presence, negative = support for trait absence. Interpretation of log-Bayes factors is based on Kass and Raftery’s (1995) modification of Jeffreys (1961, Theory of probability. 3rd edn. Oxford Univ. Press, Oxford, UK.): 0 to 2, barely worth mentioning; 2 to 6, positive; 6 to 10, strong; >10, very strong. Boldface numbers following species names indicate Volvox developmental programs following Desnitski (1995).

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Volvox 2015: biophysics

In a session chaired by Ray Goldstein, we heard about recent advances in the biophysics of Volvox and Chlamydomonas. Over the last decade or so, Volvox has proven to be an experimentally tractable model system for several questions in hydrodynamics and flagellar motility. Volvox colonies can be grown in large numbers (even by physicists!), clonal cultures have relatively little among-colony variation, and they are large enough to be manipulated in ways that most single-celled organisms can’t. Furthermore, their simple structure accommodates the kind of simplifying assumptions physicists are fond of, leading Kirsty Wan (among others at the meeting) to refer to them as “spherical cows.”

In a series of papers, Douglas Brumley and colleagues have explored flagellar dynamics in Volvox carteri. Amazingly, these studies have shown that the synchronized beating of V. carteri‘s ~1000 pairs of flagella is entirely due to hydrodynamic coupling. In other words, in spite of the apparent high degree of coordination among the flagella of separate cells within a colony, no actual coordination among cells takes place. Synchronization emerges from indirect interactions mediated by the liquid medium. An elegant demonstration of this is shown in Brumley et al.’s 2014 eLife paper, in which somatic cells were physically separated from a colony and held at various distances from each other. Despite there being no direct physical connection between the cells, they beat synchronously when close together, with a phase shift that increased with increasing cell to cell distance:

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