Friday, February 23, 2024

Predicting Speciation?

(posted by Andrew on behalf of Marius Roesti)

Another year is in full swing. What will 2024 hold for us?

Nostradamus, the infamous French astrologer, is well known for his projections into the future. Some 500 years ago, he also made a series of predictions for 2024. He wrote, for instance, “Red adversary will become pale with fear, putting the great Ocean in dread”, and “The dry earth will grow more parched, and there will be great floods when it is seen".1 These vague predictions that lack a rigorous rationale and are quite open to interpretation (have a go at it!) are probably better called “prophecies”. In contrast, the scientific enterprise has led to a very different quality of predictions. For example, today's astronomy predicts with stunning precision a total solar eclipse for parts of North America on 8 April this year. According to NASA, "... the first location in continental North America that will experience totality is Mexico’s Pacific coast at around 11:07 a.m. PDT. (...) The eclipse will exit continental North America on the Atlantic coast of Newfoundland, Canada, at 5:16 p.m. NDT". 2 Based on NASA's past predictive success we can confidently mark this eclipse in our calendars. As of today, however, meteorology cannot predict whether the weather conditions will indeed allow us to witness the eclipse from Earth. In this respect, a lot of uncertainty remains.

In many life situations, we base our decisions and actions on their predicted consequences. Yet, predictions are also indispensable in fundamental sciences where interests center on understanding how our universe works, rather than assisting with practical life problems. We recently asked some colleagues why we want to predict things in science and often heard something like "because this will tell us whether we got it right or not". – This made us think. If true, what does this mean for a field of research still struggling with making accurate predictions?

(And now for some shameless self-promotion!...)

This question marked the starting point for our essay3, which now appeared online and will be part of a special volume on "Speciation" in CSH Perspectives in Biology. To start, it seems essential to distinguish between two types of scientific predictions because they fundamentally differ in their function and value: in fundamental research, we are mainly interested in "causal predictions", not "correlational predictions". We then identify the three fundamental challenges for making accurate causal predictions in speciation research and discuss which of them are theoretically surmountable. Don't despair, there is hope! We also outline how these and further insights (more in the paper!) could shape future speciation research – namely toward a Standard Model – as well as related research in ecology and evolution.

Indeed, although tailored to speciation research, our essay connects with and easily translates to scientific disciplines beyond this field. We believe there are benefits for many of us in a deep consideration of scientific predictability, whether empiricists, theoreticians, or folks drawn to the philosophy of science. Perhaps even Nostradamus would have found interest in this read. While the fundamental topics we discuss in the essay are not new, we use an integrative and somewhat unorthodox approach – including a thought experiment with an Orrery and a Speciation Machine (see figure below) – to hopefully stimulate not only vivid and fun but also fruitful discussions. In fact, our (many) discussions on predictability have led us to organize a symposium on this topic at this year's joint ESEB/Evolution conference in Montreal (stay tuned for it!).

Our paper well complements and extends Andrew Hendry's recent paper on "Prediction in Ecology and Evolution"4, and these two papers may provide a nice back-to-back read for students, journal clubs, or coffee-break discussions. Below is the abstract of our paper. Should you have trouble accessing it in full, don't hesitate to let me know and I can email you a copy (you should also be able to access the full paper via my personal homepage).


And folks in North America, don't forget to mark 8 April in your calendars for an astronomical spectacle because it won’t happen there again for the next 9 years (3278 days, to be precise)!

References

1. Nostradamus, M. Les Proph├ęties. Lyon, 1555.

2. From https://science.nasa.gov/eclipses/future-eclipses/eclipse-2024/where-when/ (accessed 28 January      2024)

3. Roesti M, Roesti H, Satokangas I, Boughman J, Chaturvedi S, Wolf JBW, Langerhans RB. Predictability, an Orrery, and a Speciation Machine: Quest for a Standard Model of Speciation. Cold Spring Harbor Perspectives in Biology 2024 Feb 12:a041456. doi: 10.1101/cshperspect.a041456. Epub ahead of print. PMID: 38346860.

4. Hendry A. Prediction in ecology and evolution, BioScience, Volume 73, Issue 11, November 2023, Pages 785–799, https://doi.org/10.1093/biosci/biad083

Tuesday, February 20, 2024

Sticklestock center

"There are two kinds of readers.  Those who have read the Lord of the Rings.  And those who are going to."


There are two kinds of biologists.  Those who have worked with stickleback. And those who are going to.  

If you count yourself in the former category, we have good news. You can now buy stickleback through a non-profit center.  The Stickleback Stock Center (aka Sticklestock) at the University of Connecticut provides eggs, juveniles, adults, cell cultures, and associated microbes for research and education. We can do microinjection of CRISPR so you don't have to. You can place orders here:

https://www.sticklestock.com/store-1




If you count yourself in the latter category, even better news: not only can you buy stickleback for research, but the sticklestock.com website provides detailed protocols to help you get started with husbandry, breeding, field work, lab work, spatial transcriptomics, and more, through our protocols page:

https://www.sticklestock.com/protocols

Our goal is to facilitate adoption of this useful research model organism, both by supplying animals (or tissues), and advice to ease the transition.

Why have a stock center? A number of reasons motivated us to start this initiative. 

First, stickleback are highly seasonal animals that breed in mid-spring (depending on where you go). If you want embryos another time of year, you are out of luck. By offering a stock center we hope to provide a year-round source of samples.  

Second, field work is expensive and time-consuming. You need flights, lodging, rental cars, permits, traps. You need to ship fish which can turn into a major hassle when crossing international borders.  We typically do field work at just one location at a time (e.g., this summer I'll go to Vancouver Island for two weeks), which makes it hard to create crosses between geographically far-flung populations. A stock center provides a cost effective alternative, saving researchers time, expense, and reducing carbon footprints.

Third, when we study wild populations we are studying a moving target. For example, my lab has worked on Gosling Lake on Vancouver Island for 20 years now. During that time the population has seen a major evolutionary change leaving genome-wide alterations in allele frequencies, and large allele frequency change at the gene I care most about (spi1b). A stock center population may also evolve, adapting to culture enviroments in aquaria, but provides a stable genotype for future study. Moreover, multiple labs can readily study the sample genotypes facilitating collaboration and replication.

Fourth, we rarely have the option to work with populations that have genome sequences before we ever begin. The stock center plans to work primarily with populations where we already have some whole genome sequence data, or acquire some early on during culture. This allows us to offer our customers genotype-guided choices of populations to work with, an unusual opportunity for a wild vertebrate model system.

We hope the stock center grows and provides a sustained resource for stickleback researchers, current and future. If you are thinking of trying out stickleback research, get in touch! Only through sustained orders will we convince funding agencies that we have the capacity to become a self-sustaining program that can provide long-term support to the community. 


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