Aquatic science orgs oppose changing WOTUS

The Trump administration is expected to announce reductions to the waters protected by the Waters of the United States (WOTUS) rule in a couple of hours. The change is expected to remove at least some wetlands, ephemeral streams, and headwaters streams from the waters covered by the rule.

According to MSNBC,

Mark Ryan, a lawyer at Ryan & Kuehler PLLC who spent 24 years as a clean water expert and litigator at the EPA, said water systems called headwaters in high regions of the country could lose protections under the new definitions being proposed by the Trump administration.

“I think the mining is going to benefit from this because mines tend to be up in the mountains near headwater systems,” Ryan said.

Miners may no longer need to apply for a permit before pushing waste from operations, such as rubble from mountain-top coal mining in the eastern United States, into some streams.

Howe Brook

Headwater stream in Baxter State Park, Maine.

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Convergence part 6: the deepest of deep homologies

You are more closely related to a mushroom than a kelp is to a plant. It’s strange to think about, but it’s true. Kelps seem very plant-like, with their root-like holdfasts, stalk-like stipes, and leaf-like blades. But kelps are brown algae, part of the stramenopile (or heterokont) lineage of eukaryotes, which are very distant from the land plants and their green algal relatives, all of which are within the archaeplastida (the direct descendants of the primary origin of chloroplasts). Mushrooms (fungi) and humans (animals), on the other hand, are both opisthokonts, practically cousins at the scale we’re talking about.

Pawlowski 2013 Fig. 1

Figure 1 from Pawlowski 2013. Deep phylogeny of eukaryotes showing the position of small eukaryotic lineages that branch outside the seven supergroups (modified after Burki et al. 2009; drawings S Chraiti). You are represented by a fish, which at this scale you might as well be.

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Ulvophyte multicellularity: the sea lettuce genome

Ulva

Sea lettuce (Ulva sp.), Jericho Beach, Vancouver, BC, February 28, 2011.

David Kirk called the Chlorophyte green algae “master colony-formers” because multicellularity has evolved so many times within this class:

Although members of most chlorophycean genera and species are unicellular flagellates, multicellular forms are present in 9 of the 11 chlorophycean orders (Melkonian 1990). Multicellularity is believed to have arisen independently in each of these orders, and in some orders more than once.

In contrast, multicellularity has probably only evolved once or twice in the probable sister group of the Chlorophyceae, the Ulvophyceae. So when numbers like 25 get thrown around for the number of times multicellularity has evolved, something like half of those times were in the green algae.

We know a lot less about how multicellularity evolved in the Ulvophyceae than we do in the volvocine algae within the Chlorophyceae. A big step forward in understanding ulvophyte multicellularity happened last week, though, with the publication of the Ulva mutabilis genome.

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A is for Algae

I got my copy of Jillian Freese’s A is for Algae earlier this week. Freese, a Ph.D. candidate at the University of Rhode Island, says the book is “Part birthday gift. Part #scicomm. Part stress relief.” It’s full of watercolor paintings of algae, mostly seaweeds but with some phytoplankton as well. Each species (one for each letter of the alphabet) is presented with its scientific name, usually a common name, habitat and biogeographic information, and some interesting factoids.A is for Algae

Warning: spoilers below the fold.

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Multicellularity in Science

I spent the last week of June backpacking in Baxter State Park, Maine. When I finally emerged from the woods, my first stop was Shin Pond Village for a pay shower, a non-rehydrated breakfast, and free internet access. Among the week’s worth of unread emails were a nice surprise and a not-so-nice surprise. The not-so-nice surprise was a manuscript rejected without review; the nice surprise was a new article by Elizabeth Pennisi in Science, which came out when I was somewhere between Upper South Branch Pond and Webster Outlet.

Upper South Branch Pond

Upper South Branch Pond, Baxter State Park, Maine. I spent two nights here.

The article, for which I was interviewed before Baxter, synthesizes recent work across a wide range of organisms that suggests that the evolution of multicellularity may not be as difficult a step as we often assume:

The evolutionary histories of some groups of organisms record repeated transitions from single-celled to multicellular forms, suggesting the hurdles could not have been so high. Genetic comparisons between simple multicellular organisms and their single-celled relatives have revealed that much of the molecular equipment needed for cells to band together and coordinate their activities may have been in place well before multicellularity evolved. And clever experiments have shown that in the test tube, single-celled life can evolve the beginnings of multicellularity in just a few hundred generations—an evolutionary instant.

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Origins of the sexes: Eudorina and Yamagishiella

Volvox and the volvocine algae have long been a model system for understanding the evolution of multicellularity and cellular differentiation, but more recently they’ve emerged as an important model for the evolution of males and females. Sperm-producing males and egg-producing females have evolved independently in most multicellular lineages, so understanding how and why this happens is crucial for understanding the evolution of complex life.

It’s a near certainty that the unicellular ancestors from which animals, plants, fungi, seaweeds, and other complex multicellular organisms evolved were isogamous. In other words, they were capable of sexual reproduction, but the gametes that fused to form a zygote were the same size (“iso” – equal; “gamous” – gametes). In each of these lineages, large and small gametes evolved, resulting in a condition referred to as anisogamy (unequal gametes).

One really interesting thing about anisogamy is that unlike other forms of cellular differentiation, which result from non-genetic differences, the differences between sperm-producing males and egg-producing females are often genetically controlled. The most familiar way this happens is through sex chromosomes, such as the XY system in most mammals and the ZW system in birds, but there are lots of variations on this theme (check out the duck-billed platypus for an odd example).

Last month Takashi Hamaji and colleagues reported new results related to the evolution of anisogamy in the volvocine algae. The article, in Communications Biology, describes the genetic basis of sex (or mating type) determination in two volvocine species, isogamous Yamagishiella and anisogamous Eudorina. Apart from this difference in gametes, Yamagishiella and Eudorina are otherwise very similar:

Hamaji et al. 2018 Fig. 3

Figure 3A&B from Hamaji et al. 2018. Sex induction and associated gene expression alternations in isogamous Y. unicocca and anisogamous Eudorina sp. a, b Asexual and sex-induced individuals of opposite sexes of Y. unicocca (plus/minus) (a) and Eudorina sp. (female/male) (b). Mating reactions (mixed, right panels) occurred after mixing induced cultures of the two sexes (middle panels). In Y. unicocca (a), clumping of the colonies and release of single-celled isogametes (arrowheads) were observed 1 h after mixing. In Eudorina sp. (b), sex induction treatment resulted in the formation of sperm packets and the packet dissociated into individual sperm that penetrated into a female colony (arrowheads) within 16 h after mixing. Scale bars, 20 µm.

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Clues to the evolution of multicellularity from Tetrabaena

One development I’m excited to see among the Volvox community is an increased focus on Tetrabaena, one of the smallest and simplest of the colonial volvocine algae. The one species in this genus, Tetrabaena socialis, was classified as Gonium until 1994, when Hisayoshi Nozaki and Motomi Itoh revised it not only to a new genus but a new family, the Tetrabaenaceae.

Nozaki & Itoh 1994 Fig. 10

Figure 10 from Nozaki & Itoh 1994. Summary of the phylogenetic relationships within the colonial Volvocales inferred from cladistic analysis based on morphological data.

Their classification was based on morphological characters, but the backbone relationships, Tetrabaenaceae sister to Goniaceae + Volvocaceae, have subsequently been supported in several independent analyses using genetic data.

In 2013, very much to my surprise, Yoko Arakaki and colleagues showed that the (typically) four cells of Tetrabaena are connected by cytoplasmic bridges (this means that some of the ancestral character state reconstructions I did in grad school need to be revised). Their detailed analyses of Tetrabaena morphology and development are a valuable resource for comparative studies.

Now, in addition to the morphological data, we also have complete sequences for both organelle genomes (mitochondria and chloroplast) and for the nuclear genome. Jonathan Featherston and colleagues published the organelle genomes in 2016, and their new paper in Molecular Biology and Evolution describes the nuclear genome.

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Volvox 2017: Vexed Volvocines

Zach Grochau-Wright

Zach Grochau-Wright

Zach Grochau-Wright has kindly given me permission to print the haiku he presented at the Volvox 2017 meeting in St. Louis. Zach may be the most prolific artist in the obscure sub-genre of volvocine poetry, having previously written and performed “Volvocine rap” at the Volvox 2015 meeting. Here it is in its barely-longer-than-his-name entirety:

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Evolution of outcrossing and selfing

Sex is costly. You could die trying to find a mate. Your mate could kill you, or give you a disease. You could be unable to find a mate in the first place, in which case you’d be better off if you could reproduce asexually. Even without those risks, though, even in a simple genetic simulation, sexual reproduction means you only pass on half of your genes to your offspring.

So why do it? We know that it’s possible to reproduce without sex; lots of things do. It’s not just bacteria and protists, either: asexual reproduction occurs in some plants, insects, snails, amphibians, and reptiles, among many others. The logic of natural selection suggests that sex must confer some benefit that outweighs all the costs, at least in some situations. Essentially all of the proposed benefits of sex have to do with outcrossing, or mixing your genes with those of another, genetically distinct, individual.

Nevertheless, a lot of things that reproduce sexually do so without outcrossing. This is especially common in plants, where it’s called “self-pollination” or just “selfing.” Selfing is thought to provide short-term advantages relative to outcrossing–basically by avoiding the costs I’ve listed above. However, selfing also doesn’t provide most of the benefits associated with sex, so it’s thought to be a bad strategy in the long term. This leads to selfing being thought of as a “dead-end” strategy: the short-term advantages make it unlikely that a selfing species will return to outcrossing, and the reduced genetic variation produced by selfing make diversification less likely.

Erik Hanschen and colleagues have tested these predictions in the volvocine algae (I’m among the “colleagues,” as are John Wiens, Hisayoshi Nozaki, and Rick Michod): do selfing species ever return to outcrossing, and do they have a lower rate of diversification than outcrossing species? Both mating systems exist within the volvocine algae, and so they make a good test case. Roughly speaking, the term heterothallic refers to outcrossing species and homothallic to selfing species:

Hanschen et al. Fig. 1

Figure 1 from Hanschen et al. 2017. Diversity of mating systems in the volvocine green algae and their respective life cycles. (A) In outcrossing (heterothallic) species, distinct genotypes (male on left and female on right) sexually differentiate producing either eggs or sperm. A diploid zygospore (red) is produced after fertilization. Sexual offspring hatch and enter the haploid, asexual phase of the life cycle. (B) In selfing (homothallic) monoecious species, a single genotype is capable of producing both gamete types. Upon sexual differentiation, each sexual colony produces both sperm and eggs. (C) In selfing (homothallic) dioecious species, a single genotype sexually differentiates, producing either eggs or sperm, but not both within the same colony. Cartoons in panels (A–C) are shown with anisogamous, Volvox-like morphology for illustrative purposes only.

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