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). Personally, I (Will) think it looks a bit like a scene from Interstellar if you squint a little. That's not a comment on the science; I just really enjoyed Interstellar.

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!

Lynsey McInnes

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.

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!


How does ecological disturbance influence genetic diversity?

Banks et al. TREE 28(11): 670-679. How does ecological disturbance influence genetic diversity?

How disturbed are your genetics? From Banks et al.

How disturbed are your genetics? From Banks et al.

Will Pearse

Will Pearse

Disturbance is a topic very close to my heart (that’s meant to be a physiology joke), mostly because I get very annoyed when people don’t define precisely what they mean by it. So I was very heartened to read this review, where the authors discuss the various temporal and spatial scales of disturbance, and also because it’s a very nicely written paper.

Disturbance, within certain conditions, can be part of the background homogeneity of a system, and the authors are keen to stress that in this paper. I was a little surprised to not find mention of the intermediate disturbance hypothesis (even though some find it controversial), since it’s so appropriate in this context. I found figure 1 (partially reproduced above), where the authors go through some case studies of what different kinds of disturbance look like, quite helpful in reminding me that disturbance can be lots of different things, and it can have lots of different effects (not always bad). However, that figure 1 is made up of case studies reflects our lack of a coherent framework to structure how we think about disturbance. Moreover, the right hand side of the figure (which I cropped out, sorry!) talks about two case studies that involve “metapopulation” and “patch dynamics”; this makes a lot of intuitive sense to me, but on reflection I find that kind of weird. Metapopulation theory is a concept humans have generated, it’s not a thing that biological systems recognise, and I think it might be better to categorise systems on the basis of properties they share rather than how we find it easiest to model them.

So what would such a categorisation look like? After reading this paper I think disturbance severity, duration, and extent (bear with me) are three important axes. With ‘extent’ I want to incorporate the ability to temporally and spatially escape a disturbance; spatially means whether the disturbance is everywhere and whether you can move to avoid it, and temporally that means whether the disturbance happens very often or very infrequently and would probably incorporate seed bank effects. I’m sorry ‘extent’ is such a poor descriptor; I’m decaffeinated and would appreciate better suggestions! I’ve very deliberately chosen to put space and time on the same axis; you might prefer to split them. You might also prefer to add predictability as another axis; I don’t, not because I don’t think it’s important, but because I think a system’s history (which, in turn, incorporates predictability) affects quite a lot and the other axes mostly capture what the system has been doing in the past. Not a lot about genetics in this post (sorry!), and instead a framework that almost certainly already exists somewhere and I’ve forgotten I’ve read it. Please do tell me where!

Lynsey McInnes

Lynsey McInnes

I had high hopes for this paper. I’m attracted to any paper that deals with intraspecific variation head-on and am well aware that intraspecfic variation affects and is affected by processes occurring on varying spatial and temporal scales. So, a paper dealing with how disturbance affects genetic diversity seemed right up my street. I was curious about the direction the paper would take as my feeling was genetic diversity is generally quite hard to measure particularly in non-equilibrium populations (such as those that have been disturbed) and assigning particular genetic signatures to historical events (‘disturbances’) is notoriously difficult as not only can a range of different events leave the same genetic signature, the same event can leave different signatures depending on the ecology and population structure of the species involved.

It was good for my ego to find that the authors largely confirmed my suspicions of these issues, but sad for the paper that there seems no easy way out.

It seems that the current state of understanding is that we live in an increasingly ‘disturbed’ world . Events such as tsunamis, fires and grazing impact nearby populations, reducing the number of individuals and thus most likely (at least) point estimates of genetic diversity and the challenge is to recognise the types of populations/species that will find recovery from such impacts difficult or impossible (if one is interested in conserving viable populations, otherwise all impacting populations are interesting, for instance, what kinds of species can you bombard with disturbances and they bounce right back to pre-disturbance levels of abundance and genetic diversity?). It seems however, that little research has focussed on the relationship between disturbance and genetic diversity and that there are many outstanding questions.

The second half of this paper gave a helpful overview of these outstanding questions and laid out some helpful ways forward. Namely, and understandably, the integration of multiple sources of data (event type, species’ traits, samples across the range and through time, etc.) will help to unravel the impact, or non impact, of putative disturbances on genetic diversity and, more importantly, what these effects mean for the longer term survival of species and/or communities. In fact, the paper lists FOURTEEN outstanding questions linking disturbance and genetic diversity and all of these are interesting. It would have been nice if these had been dealt with in more detail in the paper, perhaps focussing on a couple and on real routes forward to addressing them.

Maybe I missed this in the paper, but I also felt that what was missing was strong evidence that one expects any general link between disturbance and genetic diversity. As next gen sequencing gets cheaper and more accessible for non-model organisms, it will become trivial to look for these links, but, I feel, we need to know what we are looking for before we go looking for it. The general view is that more genetic diversity per population is better to ensure buffering against a variety of disturbances, but the authors show this is not always the case. Individuals can come from beyond the disturbance centre to make up for lost individuals and/or diversity. To predict this rescue effect one has to have a bigger picture encompassing knowledge of the genetic diversity of multiple populations within and beyond the disturbance centre. Are there enough individuals for recovery and do these individuals possess the desired adaptations? (So, I might differ from Will in thinking metapopulation theory might be helpful here).

I absolutely believe that intraspecific variation within and between populations in terms of genes and ecology must be considered if we hope to understand how populations will cope in the face of point disturbances and longer term environmental fluctuations. This paper drove home to me quite how difficult this endeavour is going to be.

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