The unappreciated animals of science

Would you believe it – I actually forgot that I had a blog for a few of weeks. I guess I was busy?

If you don’t work on a particular organism, you tend to forget that each has its own history outside of the laboratory. Catherine Dulac has a great video wild-caught mice: whereas laboratory strains are sedentary, moseying about their cage without a care in the world, wild-caught mice are little ninjas, running around and jumping off the sides. These ain’t the same creatures.

eLife has a good series on the natural history of model organisms. Right now they have C. elegans, zebrafish, and E. coli, though I expect there will be more.

On nasty E. coli:

In 1884, the German microbiologist and pediatrician Theodor Escherich began a study of infant gut microbes and their role in digestion and disease. During this study, he discovered a fast-growing bacterium that he calledBacterium coli commune, but which is now known as the biological rock star that is Escherichia coliE. coli‘s relationship with a host literally begins at birth. Newborns are typically inoculated with maternal E. coli through exposure to her fecal matter during birth and from subsequent handling. Although perhaps disconcerting to ponder, this inoculation seems to be quite important. Indeed, E. coli becomes more abundant in the mother’s microbiome during pregnancy, increasing the chances of her newborn’s inoculation…

The external world was long thought to be so harsh as to preclude E. coli‘s growth outside of its host. While a tiny minority might eventually reach a new host, most cells were expected to eventually die. This is the basal assumption behind using the presence of E. coli as an indicator of fecal contamination. However, recent studies have shown that E. coli can, in fact, establish itself as a member of microbial soil, water, and plant-associated communities

On fishies:

Field observations of zebrafish behavior are few and anecdotal, and so much of what zebrafish do in nature has to be inferred from their behavior in the lab…Interestingly, wild-caught and lab fish (both previously imprinted on the ‘wild type’) have similar preferences for prospective shoaling partners…Lab strains of zebrafish spawn all year round, but breeding in the wild occurs primarily during the summer monsoons, when ephemeral pools appear; these presumably offer plenty to eat and some shelter from currents and predators.

Analyses of wild zebrafish suggest a reason for the discrepancies: these fish have a major sex determinant (WZ/ZZ) on chromosome 4—which has features similar to sex chromosomes in other species—yet this determinant has been lost from lab strains (Wilson et al., 2014). This suggests that founder effects, or domestication itself, led to seemingly ad hoc systems employing multiple sex determinants, probably of small original effect in the wild.

On wormies:

This species was originally isolated in rich soil or compost, where it is mostly found in a non-feeding stage called the dauer. More recently, feeding and reproducing stages of C. elegans have been found in decomposing plant material, such as fruits and thick herbaceous stems. These rotting substrates in their late stages of decomposition provide abundant bacterial food for the nematode…Population demographic surveys at the local scale in orchards and woods indicate that C. elegans has a boom-and-bust lifestyle. C. elegans metapopulations evolve in a fluctuating environment where optimal habitats are randomly distributed in space and time… Over the year, in surveys performed in France and Germany, C. eleganspopulations in rotting fruits typically peak in the fall, with proliferation possible in spring through to early winter…

If not with E. coli, it is noteworthy that C. elegans shares its rotting fruit habitat with two other top model organisms, Drosophila melanogaster and Saccharomyces cerevisiae…A specific association is actually found between another Caenorhabditis species and another Drosophila species: this nematode species, C. drosophilae, feeds on rotting cactus in desert areas and its dauer juveniles use a local Drosophila species as a vector to move between cacti.

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The model species

At Molecular Ecologist, Jacob Tennessen asks whether people are the unsung model species of molecular ecology:

Non-invasive genetics and “natural experiments” are employed to make inferences about evolutionary history, behavior, fitness, and other aspects of natural history. These same restrictions also apply to humans: breeding humans in the lab is as ethically fraught as it is logistically challenging. But, the difference between studying humans and, say, elephant seals is that the established knowledge base for humans is much greater. The combined size of available population genetic datasets in humans is a billion-fold larger than for most species, even some that have already been the target of molecular ecology studies, and these human data are much better annotated and validated…

So, what are the most important things we have learned from studying our own molecular ecology? Perhaps the primary lesson from human population genetics is that intergroup differences that seemed substantial to our subjective brains, like between Africans and Europeans, turned out to be minor. There are few if any fixed autosomal differences between continental groups, and the phenotypic markers we are inclined to use, like skin color, are encoded by some of the most divergent loci, making them a poor proxy for overall evolutionary distance. A related major lesson is the surprising ubiquity of “soft sweeps,” or positive selection acting on standing variation. Unlike the classic model of a newly arisen mutation rising quickly to fixation, most geographically local adaptation in humans comes from more subtle changes in the frequency of existing alleles, hence the dearth of fixed differences. A third lesson is that the most genetically diverse human populations are found in our ancestral homeland in sub-Saharan Africa, with basal populations such as the San showing particularly high polymorphism.

These are all excellent and under-appreciated points. In cognitive neuroscience, is there any better model organism than the human brain? One of the limiting factors in incorporating genetics into human neuroscience is the paucity of relevant biological data. We know, roughly, that certain SNPs in genes like DRD4 or SERT can change dopamine or serotonin function, kind of, but it’s very non-specific, and regulation of individuals genes varies across brain region. It’s difficult but I’m highly optimistic about the future of humans as a model organism in molecular neuroscience!

I also wonder whether the lessons of evolutionary ecology are sufficiently well-known among theorists of neural function, especially the influence of ‘soft sweeps’. I get the sense that the answer is definitely no.

More importantly, though, five points to gryffindor for the first comment: ‘the speaker (Lawrence Hurst, I think) started with “humans are an excellent model system for understanding Drosophila’.