ARTICLE: How does tool use evolve in animals?

Data-Driven Inference Reveals Distinct and Conserved Dynamic Pathways of Tool Use Emergence across Animal Taxa, iScience 23 101245 (2020)

There are some wonderful examples of animals using tools. Octopuses block oyster shells open with coral; boxer crabs wave captive anemones for defense and food capture; captive dolphins use feather to wipe clean their aquarium windows. A while ago, we saw this excellent infographic in National Geographic, and got interested in these data. Do different families of animals learn to use tools in completely different ways? Or are there some general ("universal") principles behind how animals learn to use tools?

There is, of course, a big and fascinating literature on tool use, but we found rather few studies attempting a quantitative comparative analysis across bilaterian animals. To address other evolutionary questions, we've developed HyperTraPS (hypercubic transition path sampling), a statistical approach for learning the "pathways" of evolutionary processes. That is, which events occur before and after which other events in an evolving system? Does feature A always evolve before feature B? We used HyperTraPS to ask about the orderings with which different types of tool use appeared in animals. For example, do animals always learn to "poke" before they learn to "dig"? Do all animals learn tool use in the same order, first A then B then C..., or does it vary across species?

We found some answers that we think are quite interesting. There seem to be some quite deep similarities across animal species in how tool use evolves. Types of tool use like "affixing" and "throwing" are almost universally acquired early; types like "cutting" and "symbolising" are acquired late and rarely, only by primates. The environment and animal family influences the structure of these pathways: aquatic organisms seem to discover "waving" tool use relatively early, for example, and primates discover tools that "block" relatively late.

(A) The inferred pathways of tool use emergence across animals. The size of a blob gives the probability that that mode of tool use (on the horizontal axis) is acquired at that stage (on the vertical axis) of a species' discovery of tool use types. (B) Sample evolutionary pathways of tool use, with individual animal lineages illustrated at the positions corresponding to the modes of tool use they have discovered.

Of course, there's a lot of uncertainty about any analysis like this. Are we talking about wild or captured animals? What if we just haven't observed some types of tool use? We attempted to address several such questions with our analysis and showed that our overall results were quite robust with respect to these uncertainties. HyperTraPS fully describes the uncertainty in its outcomes, helping interpretability. We hope that our results help at least to suggest some possible principles and points for further investigation in this fascinating topic. You can read more in iScience here.

ARTICLE: What makes mitochondria selfish, and when do selfish ones win?

MtDNA sequence features associated with ‘selfish genomes’ predict tissue-specific segregation and reversion, Nucleic Acids Research 48 8290 (202)

Mitochondria, the power stations of the cell, are in some senses like people in a company. The company needs several people to contribute if it is to survive. Some people may work hard and contribute lots to the company. Others may selfishly slack off and rely on others doing the work.

The cell needs mitochondria to produce ATP, the chemical that powers many important processes. But there is evidence that some mitochondria are more selfish, and some less so, than others. Unselfish mitochondria produce machinery which helps produce ATP. Selfish mitochondria prefer to replicate, copying their DNA and contributing less to the cell. Interestingly, at the molecular level, there is something like a "switch": a mitochondrion either takes steps to produce useful machinery, or takes steps that will help it replicate.

We were interested in why different mitochondria choose different positions of this switch, and what is a good "strategy" for mitochondria under different conditions. We built a simple model of this behaviour to understand it. Unsurprisingly, we found that selfish mitochondria -- favouring replication, and contributing less to the cell -- profilerate over unselfish ones in cells where there's little pressure to co-operate. As they replicate more, selfish mitochondria eventually come to dominate such cells. Where there is cellular pressure, however, unselfish mitochondria may win out. This is because cells full of selfish mitochondria won't perform adequately, and the whole cell and all its mitochondria will die -- leaving those cells with more unselfish mitochondria remaining.

What do we mean by "cellular pressure"? Well, if some type of cells never die, clearly the latter event can't happen, and we'd expect selfish mitochondria to win. If cells die regularly, perhaps there's more capacity to select those filled with unselfish mitochondria. We looked at different tissues where cells die with different rates, in mice where cells had two different types of mitochondrial DNA (mtDNA). We found a consistent pattern where one type of mtDNA proliferated in slow-dying cells and the other proliferated in fast-dying cells. Why different mtDNA types "win" in different tissues is a big question (which we've looked at before!), and it looks like this might help explain some of these differences.

(A) Sequence features may make different mtDNA types more "selfish" (favouring replication) or "unselfish" (favouring the production of useful machinery). (B) Our theory shows how, depending on cellular pressures, one or the other strategy can be favoured, leading to selection for one or the other mtDNA type.

We also asked what it is about a particular mtDNA sequence that might make it more or less selfish. Based on how mtDNA produces useful machinery, and how it replicates, we hypothesised that some features in the so-called "control region" of mtDNA may influence selfishness. Using sequence information, we found that these features tied quite neatly in with the observations in these mouse models, and also in (more limited) observations from human cells. While certainly not resolved, this picture suggests a link between sequence features of mtDNA, cellular selfishness, and proliferation differences across different tissues. You can read more (for free) in Nucleic Acids Research here.