A Neutral Theory for Interpreting Correlations between Species and Genetic Diversity in Communities

Laroche et al. The American Naturalist 185(1): 59-69. A Neutral Theory for Interpreting Correlations between Species and Genetic Diversity in Communities

Figure 4 from Laroche et al. The Species-Genetic Diversity Correlation plotted against mutation rate (m) and carrying capacity (K). Ignore the white splodges; they’re unimportant for our purposes. Hopefully we’ve just nerd-sniped you into reading the paper!

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Lynsey Bunnefeld

Oh the dangers of picking a paper because you like the keywords and finding them cooked in a different way to you had imagined in your head. I have a slow-burning interest in how thinking about intraspecific variation can help explain interspecific patterns of diversity, turnover, etc, and this paper’s keywords fall right into that gap…

Here, the authors are interested in understanding why you often find, or expect to find, positive correlations between genetic diversity of a focal species and species diversity in the same area (i.e., not quite the same thing). They elegantly explain accepted thinking on the effects of local competition and connectivity and size of sites in a metacommunity as being the factors underlying these expected/often observed patterns.

The paper is concerned with adding the omitted factor of mutation ‘regime’ into the mix. If mutation occurs at the same rate as migration among sites, the expected correlation between genetic and species diversity could break down. I’m not going to lie, the way the authors get to this outcome remains somewhat opaque to me. My general understanding is that when mutation rate is high, the impact of migration among sites is less predictable as there will be a greater variance in what amount of diversity is transferred among sites and this leads to unpredictable knock-on effects on genetic diversity-species diversity patterns. How, you might ask, how indeed?

What I did like about this paper, probably because it harks back to what I liked about the keywords is the incorporation of more actual genetics into the model. Mutation regime is a necessary addition to thinking about genetic diversity and, as the authors rightly point out it is going to be easier (and at the same time much more complicated) to deal with as genomic data pours in. We appear to be on the cusp of understanding how these different levels of diversity impact each other and it’s mega exciting! Models such as this one are pretty awesome, and set the stage for the next step which would be incorporating mutation rate heterogeneity, including at selected loci. Population genetics has the machinery to deal with this variation, we just might need a bit more crosstalk with ecologists and theoretical biologists to get to more refined characterisations of patterns (if there are any) at the macro scale.

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Will Pearse

Maybe this is off-topic, but I was dreading reading this paper because these sorts of analyses terrify me. I wasn’t familiar with the ‘ODD model‘ of describing biological models, but the authors use it to such excellent effect that my fears were completely unfounded. If you’re a theoretical person, please use this approach!

This is a paper about within-species diversity (community genetics, not community phylogenetics), and so almost by definition they cannot examine speciation processes. However, I was left wondering how speciation would interact with these dynamics; I assume it’s tricky to model because otherwise a ‘smart’ thing for a genotype to do would be to speciate and thus avoid competition with the genotypes it left behind. Perhaps you’d end up moving to a more coalsecent-esque model in which individuals’ competition strengths are a function of time since coalescence – species identity itself would be something a bit arbitrary. I’m interested because I think there are so many parallels with this model and the more Neutral Theory models (and some of the models of fitness we’ve discussed in the past). I wonder what the dynamics would look like if you just shunted some of these dynamics inside a classic Neutral model.

Presumably this sort of literature applies only to neutral alleles – if there is an allele that confers a selective advantage, then natural selection et al. kick in. Which is where I was wondering how competition steps into this framework – I think it’s at the step where new individuals are drawn (please correct me!), in which case I can see how migration and mutation rates would affect what we find. On another side-note, I particularly liked that the authors had worked sampling into their model – it made it a lot easier to draw this back to what would be expected empirically, and helped the authors make sense of how such empirical results seem to disagree with this model at first. More of this as well, please!

Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

Elena and Lenski (2003). Nature Reviews Genetics 4: 457-469. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

Local optima can hold back a population from doing the best that they could. From Elena and Lenski (2003).

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Will Pearse

This paper is more than a little beyond what I usually read, but I always enjoy going to bacterial evolution talks, and I enjoyed this. This is such a rapidly-changing field that I’m certain new things have come out – please do chime in!

I was very struck by the discussion of mutators. The idea that individuals with higher rates of mutation can, in some circumstances, be of benefit to the rest of the population is really cool. It also has a lot of implications for the constant arguments I seem to have with people over what ‘evolvability’ is: as far as I’m concerned, if there’s a thing that increases the rate of adaptation of a population, that’s an increase in evolvability, and mutators seem to be that. We talk a lot in large-organism evolutionary biology and biogeography about the importance of historical accident – that fast rates of mutation only sometimes increase the evolvability of a population, and only sometimes do such individuals come to dominate, is an excellent repeatable and predictable example of the problem. It’s nothing short of amazing that we can do accurate back-of-the-envelope calculations and figure out the odds of a particular outcome in a petri dish.

One thing I want to slightly temper some of this with is the importance of natural history in these populations. It’s all very well studying the evolution of bacteria in stationary phase and discussing how this is different from what we normally find in the lab, but stationary phase is not the normal state of affairs for bacteria. In the wild, bacteria are not transferred into new media when there’s too many of them, and the same goes for large-bodied organisms too. If we want to understand natural evolutionary processes, we need more stationary phase experiments (right? Am I being ignorant?). To paraphase someone else, we also spend a lot of time examining bacteria that cause diseases in particular environments (the human gut, for instance), and modelling their evolution in situ. The problem with this is that this isn’t what those species do for their whole natural history – if you don’t consider how those species got into that environment (water, soil, kitchen sink, etc.), or what some might call a ‘fluctuating environment’ then you’re not going to get the complete picture of the evolution of that species.

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Lynsey McInnes

This is a difficult paper to discuss because I feel like I know that there have been many advances since it came out, not least in our capacity to study mutations and their effects right down to the level of single nucleotide polymorphisms and up again to the level of whole genomes. However, my knowledge of this literature is hazy at best (but see Will’s and my first attempt at discussing experimental evolution here). I’m just going to paste in the abstract below so you know what the paper was actually about (seen as my post barely touches on it…).

‘Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.‘

What am I going to write about then? Well, I think going off on a tangent seems like the best idea. My background is heavy on macroecology (patterns! scale!) and my current work centres around exploiting neutral genetic variation among populations to infer demographic history (which I am increasingly realising can get quite close to macroecology when it wants to). So I am not accustomed to thinking about mutations that affect function or adaptation in beneficial or a deleterious ways. Selected genes are in fact the bane of my data. Although I remain unconvinced that we are ever confident that a locus is ever completely neutral.

In fact, I am quite jealous of experimental evolutionary biologists. It seems unfair that they are able to watch things (really, anything!) happen in real time whereas macro-scale analyses (macroevolution, macroecology, phylogeography, biogeography) rely on sometimes shaky sets of assumptions, occasional blind leaps of faith and (more often than not) bundling a lot of unexplained variation into historical contingency. I am a big fan of comparative and meta-analytical approaches (which I’ve advocated on many a PEGE post) where generalities can emerge on diverse topics such as prevalence of niche conservatism, latitudinal richness gradients, modes of trait evolution, even of community assembly, but there is always the niggling doubt that contingency gets in the way and overrides any signal. Wouldn’t it be great if we had five Caribbeans and could throw on five identical Anolis clones and watch what happened? Bacterial experiments can do this! So jealous!

What I’d like to see is more engagement between experimental evolutionary biologists and macro-people. How close can we get to equivalent situations? Can we apply our macro approaches to bacterial setups and see what we find? What is and is not transferable? How much does asexuality mess things up? How much does single cellularity mess things up? I am quite sure that there must be some theoretical exploration of these ideas, but I’d like to see more cross-talk among empiricists. Especially now that we can sequence anything (especially easily bacteria), let’s find out more about how comparable these systems are and what the next stage might be?