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.

[Read more…]

Convergence part 5: an embarrassment of riches

In parts onetwo, and three of this series, I showed that some intelligent design proponents have created an alternate history of biological thought, in which evolutionary biologists have only recently discovered that similar traits often appear in distantly related species. I showed that this picture is false, and I gave a sampling of quotes–from Jean-Baptiste Lamarck, Charles Darwin, Ernst Mayr, George Gaylord Simpson, Willi Hennig, and others–demonstrating that evolutionary biologists have recognized that this phenomenon is common for as long as there can reasonably be said to have been evolutionary biologists. In part four I explained why widespread convergence is not evidence against common descent, as some ID proponents have claimed.

Mivart Cover

[Read more…]

Elephants and oak trees

The Major Transitions in Evolution cover

The increase [in complexity] has been neither universal nor inevitable. Bacteria, for example, are probably no more complex today than their ancestors 2000 million years ago. The most that we can say is that some lineages have become more complex in the course of time. Complexity is hard to define or to measure, but there is surely some sense in which elephants and oak trees are more complex than bacteria, and bacteria than the first replicating molecules.

[Read more…]

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.

[Read more…]

Placozoan diversity and taxonomy

If I didn’t study Volvox, I would probably study placozoa. Placozoa are animals, but you wouldn’t know it to look at them. They look and behave very much like giant amoebae, big enough to be visible to the naked eye.

Trichoplax adhaerens

Trichoplax adhaerens. By Bernd Schierwater – Eitel M, Osigus H-J, DeSalle R, Schierwater B (2013) Global Diversity of the Placozoa. PLoS ONE 8(4): e57131. doi:10.1371/journal.pone.0057131, CC BY 4.0, Link

[Read more…]

Changing into my old genes: Betül Kaçar’s molecular paleontology

KacarTapeofLife

Betül Kaçar has posted another preprint to bioRxiv describing her work combining molecular paleontology with experimental evolution. I’ve written about Dr. Kaçar’s research, and the Discovery Institute’s bizarre interpretations, before, and I won’t be surprised if the cdesign proponentsists feel compelled to respond again.

The new preprint describes experimental evolution in E. coli bacteria genetically engineered to express an ancient protein in place of its modern counterpart. The gene encoding the protein, Elongation Factor Tu (EF-Tu), exists in two copies in the wild-type E. coli genome. Dr. Kaçar’s team deleted one copy and replaced the other with a gene sequence inferred to be similar to that in E. coli‘s ancestor from 700 million years ago.

[Read more…]