Labels: chemistry, chitons, molluscs, photos, sci-blogs, science, sunday spinelessness

For someone that writes about evolution, I don't spend much of my time talking about the 'debate' that surrounds that topic. That's probably an artifact of living in a county that doesn't allow people who are so confused about the world that they think the bible is a biology textbook to acquire any political power. But it's also because debating whether evolution happened, a fact that no serious biologists has debated since Darwin's generation and is further confirmed with each new DNA sequence, is so utterly and spectacularly boring when you compare it with some of the real debates with evolutionary biology. So here's a little something on one debate, and the land snail shells that help swing it a little towards one side.

Some of the most contentious debates within evolutionary biology are to do with how new species arise (a process we call speciation). For instance, it's not clear how much ecology* matters when it comes to speciation. Some authors argue that speciation and ecological adaptation are usually seperate processes - the second making species distinct only after speciation has separated them. Others argue that ecological adaptation can itself be an important part of the speciation process and maybe even be enough to drive species apart.

Like many ideas in evolution, this debate goes back to Darwin's time. People who really ought to know better will sometimes tell you that, despite its name, The Origin of Species doesn't have a theory of speciation. You should tell those people to read Chapter 4. Darwin did have a theory of speciation, and it explicitly placed ecological competition between newly formed species as the key to driving species apart from each other. We've learned a few things about biology since Darwin's time, and it turns out his verbal arguments don't hold up to mathematically rigorous models of the ones genes work in populations. Natural selection can't push a population apart more quickly than genetic recombination (the mixing of genes that happens in each generation) pulls it back together. So, species can't arise soley from selection. In fact, the modern conception of speciation revolves around the flow of genes between populations. If a population isn't sharing genes with others it's free to evolve independantly and take on the properties that make species distinct.

Although people have talking about gene flow with regard to speciation since Darwin's time, Ernst Mayr is probably the person most associated with establishing this idea among evolutionary biologists. Mayr took the importance of 'reproductive isolation' to its logical extremes - arguing lack of gene flow was not just a pattern that created species but actually the definition of a species (I disagree) and that speciation almost exclusively occured because of geographical barriers that keep populations apart from each other (leaving no room for selection).

But the gene-flow conception of speciation still leaves a tiny bit of room for selection as a driver of speciation. For instance, imagine a trait that could, at once, be subject to ecological competition and prevent gene flow between members that don't share the trait. Then selection would be acting to keep diverging species away form each other at the same time as adapting them to their habitat. Sergey Gavrilets, a theoretical evolutioanry biologist, called models of speciation that rely on these sort of quirks "magic trait" models, partly to represent some scepticsm that such traits could exist in the wild. But empiricists have known for a long time that these sorts of traits really are out there. For instance, many plant eating insects only mate on their host-plant. So, if two diverging species are adapting to particular hosts plants, that same adaptation process will be preventing them from mating with each other. Other examples of these magic traits include body size in fish, beak size in birds, wing colouration in butterflies and, now, shell characters in land snails.



Snails can be left- or right-handed. Or, at least, the sprial of a snail's shell can turn clockwise (making a right-handed or dextral spiral) or anti-clockwise (a left-handed or sinistral spiral) and the direction of spiraling is decided by a single gene (inherited from the mother, suggesting in may be an imprinted gene as snail's don't have sex chromosomes) . Most species are predominately right-handed and very few individuals within a species don't match the predominant spiraling direction (I only know of one exception to this rule). In fact, I've spent more time than most people looking at snails, and I've never seen a left-handed one (trust me, I check!). There's a very good reason one individuals within one species are predominately of one spiraling direction - left-handed land snails have great trouble mating with right-handed ones. Land snails are all hermaphrodites and they mate by lining up extending their gentals through a pore on the 'spiral side' of their body (if you aren't invert-phobic, there are plenty of photographs of this process here). But mirror-image snails, espacially those with relatively flat shells, struggle to line up in this way, and when they do their shells bump into each other. For this reason, 'mirror' snails (which do arise in populations all the time) struggle to reproduce and leave few descendants.

The direction in which a snail's shell coils also has ecological implications. Animals that specialise in eating snails have adapted to attacking right-handed shells. So, for instance, Pareas snakes always attack from the left and have lopsided jaws that help them work the snail out of the shell:

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You should also check odd Ed Yong's take on this study, which is predictably excellent.

*I'm sorry to do this, because I don't want to be one of tiresome people who complain about the way language changes, but the science of  ecology is something quite different from what's fast becoming the modern definition of the word. Ecology is the study of the way organisms interact with each other and their environment and (as far as I can tell) mainly involves counting a lot of things then doing some clever statistics on the resulting numbers. It's not (directly) about conservation or sustainability and it's certainly not an idea invented by advertisers who worked out adding 'eco-' to a products name and putting it in a plain box allowed them to sell it at twice the price.

Labels: environment and ecology, sci-blogs, science, snails, speciation, sunday spinelessness

If you read the Sunday post last week you'll remember that I started a little "when my brains are completely destroyed by thesis wrangling and I need a break" project, and that I'm the sort of person that takes a break from one science project by playing around with another science project. That's just how sad I am. Anyway, last I week i set out to use existing records in GenBank to compare the diversity of fungal species living on the roots of various species of tree in New Zealand. And I failed. I only managed to find records for one species, silver beech, so all I could really say was that there seemed to be a lot of different fungal species on this tree.

Inevitably, I found myself needing a break from thinking about my snails this week, so had another crack at comparing fungal diversity by host. In particular, I've filtered through hundreds of records of fungi collected from New Zealand to isolate those collected from natural southern beech (Nothofagus) forests or plantation pine forests. The mycorrhizal fungi I talked about last week are generally considered to be highly host-specific and unable to form relationships with off-host species. If that's true we should be able to see that the community of fungi recorded for each forest type is quite distinct. But how can we see that phenomenon? Last week I used a graph of the frequency of different taxonomic families to show how diverse the community living on silver beech was, but taxonomic ranks above species don't represent anything real about biology or biodiversity. I have argued species are natural units of biodiversity (even if we can struggle mightily to identify those units), but most of the sequences I've found aren't annotated down to this level (in fact, most probably represent undescribed species). So, I gave up on a 'unit of biodiversity' and instead only included sequences for a particular gene loved by fungal geneticists called the Internal Transcribed Spacer. Using just these sequences, I can make a phylogenetic tree, which attempts to relate DNA sequences to each other based on their similarity.

So here's the tree, drawn as a big circle. Each tip represents a single DNA sequence and is shaded according to the forest it comes from - brown for pine, green for beech. As you can see, the pine and the beech forests have very different fungal communities. There are whole swathes of the tree that are unique to to beech forests (although, of course, that could be an artifact of the effort to which people have sampled) and whenever you see a brown branch within a predominantly green section of the tree, that branch is substantially distinct from its beech-living relatives. (click on the image to be taken to an interactive version, where you can add information on host species or change the shape of the tree):


So that's fun. There's still a lot more that could be done with the data set. I haven't included much data about the fungi themselves - it would be interesting, for instance, to see if the fungi living in the roots of trees showed more or less specificity than the those living elsewhere. It might also be possible to use these sequences to estimate the number of species they represent using some of the new-fangled species delmitation methods the DNA Barcorders have come up with. There are also other natural forest types in New Zealand that might be interesting to include. Both Manuka and Kanuka rely have mycorrhizal fungi and including those species might help us to understand if the differences displayed above are about natural v plantation forests or about host-specificity in the fungal species.

I didn't include any code snippets today, because I've set up a github repository as an 'open record book' instead. If you're interested in the process or the code that went into this you can check it out there (though I should warn you, there's nothing very clever going on).

Labels: biopython, environment and ecology, fungi, geekery, python, sci-blogs, science, sunday spinelessness

One of my goals with these Sunday posts is to do a little to broaden the understanding of just how extraordinarily diverse the biological world is. In almost two years of writing about spineless creatures I've limited myself to animals, which, as amazing as we are, only comprise one twig in the tree of life. You can call that an institutional bias, since I'm from a Zoology Department (there are few that haven't yet been swallowed by Schools of Life Sciences) and maybe it's a necessary step to narrow the field of targets a little bit. But this is my blog, and my series, and today I want to write about fungi.

In fact, fungi are a prefect example of the gap between our everyday experience of the biological world and what's really out there. Most of us only notice fungi when mushrooms start popping up in the autumn or when the fruit we bought, and were definitely going to eat this time, starts turning furry. In fact, there might be something like one and a half million species of fungi on earth; there are deep-sea fungi, forest fungi and freshwater fungi; there are fungi that live on tree roots and others that live on human skin; there are even mind-controlling fungi that hijack the nervous system of certain ant species for their own gain:

Some fungi play important roles in ecosystems, and probably the most important of all are a taxonomically diverse group that livr in or on the roots of plants. These so called 'mycorrhizal' fungi greatly increase their host's ability to take up and process nutrients and water from the soil, while the fungi can take advantage of the plant's ability to create sugars from carbon dioxide and sunlight. Between 80 and 90 per cent of plant species can form relationships with mycorrhizal fungi (Wang and Qui 2006 doi: 10.1007/s00572-005-0033-6) and, as you might imagine, the presence or absence of mycorrhiza can have a big impact on the health of individuals plants, crops and forests.

On Wednesday, I heard David Orlovich (@davidorlovich) speak about mycorrhiza in southern beech (Nothafagus) forests in New Zealand. Beech forests form a major part of New Zealand's natural heritage, and some our most important conservation sites (Westland, Fiordland...) are covered almost exclusively by beech species. Without mycorrhizal fungi there would be no Southern Beech: seedlings raised in sterile soil simply fail to develop. David went as far as to say that we should see beech trees as giant antennae that fungi used to fix carbon from the atmosphere. I'm not sure I'd follow him quite that far, but his talk on using DNA sequences to quantify the number of fungal species associated with local silver beech forests and the the specificity of fungal species was really interesting.

It also got me thinking about a blog post by Rod Page (@rdmpage) in which he shows how we can take advantage of data that is stored in The Big DNA Database (called GenBank) but goes almost unused. Every record in GenBank has certain information attached to the DNA sequence in describes (the source of the sample, the name of the gene, a scientific paper the sequence is attached to) but the information in a given record is not limited to the required fields - researchers can add any pertinent information they want to. Researchers in biodiversity and related fields often wring their hands about the lack of any infrastructure to hold data collected on various species and taxonomic groups, but, as Rod has pointed out in the past, existing databases (and wikipedia) already contain considerably more information than we're taking advantage off.

So, when I decided I needed a break from thinking about snails this Friday night, I set out to see if there was enough information about fungal hosts in GenBank for us to start examining the fungal diversity of New Zealand forests*. You could make a start at that project using the pointy-clicky web-interface but I decided to use Biopython (a library for the Python programming language), because writing code for a project is really the best way to document what you're doing , helps make you research reproducible and allows you to pick up a project where you left it. So, the first step was finding records that corresponded to sequences from mycorrhizal fungi in New Zealand. As far as I can tell you can't search within particular submitter-defined features of a file, so here's how I did the search with Biopython's Entrez.esearch() function.

The 'ids' object collected form that search is a list of unique identifiers for sequence records that matched our search, so let's get all of those records in a sequence file and use SeqIO from Biopython to deal with them

Now the heavy lifting! We need to get the host information from each record which means looping through a bunch of attributes in the Biopython object representing that record. We want to store the data as a "one to many" relationship, since each host species might have multiple fungal species associated with it. There are couple of different ways of doing that, but I used python's very cool "defaultdict" dictionary which can create a list for each host and add new information to that list when it encounters the host.

And this is where everything went wrong. Well not quite, the search term I used found 84 records, but they were all for fungi collected from silver beech (Nothofagus menziesii) trees. So much for comparing diversity between hosts! Still, those 84 records give us a change to estimate the taxonomic diversity of fungi associated with this tree, so lets count up all the unique taxonomic names among these records:

And (dropping python for R and ggplot2) a graph (click for a larger version):

I'm not finished with this little project, I have some ideas to widen the net for fungal species next time I get really sick of snails, but even this little exercise shows some interesting things. First, silver beech have lots of fungi on their roots, and they come from lots fo different groups! It would be fascinating to know if the fungal families represented above were playing different roles in the root-tip, or if each was competing with others. Or how that make-up of the fungal biota attached to a given tree or a given forests effects its health. More importantly, GenBank is potentially a really useful way for researchers to share more than just sequence data. If people working on mycorrhizal fungi decided on a de facto standard for the way they annotated their GenBank submissions then data from hundreds of published (and unpublished) studies could be almost effortlessly combined to create a big picture of the dynamics of these important fungi. Even as it is now, there is a source of data that is almost never used by researchers or people building the various "encyclopedia of life" projects, and it doesn't take too much tinkering to see how it could be put to use.

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*Yes, I'm the sort of person who takes a break from science by doing some other science. On a Friday night. What of it?

Labels: biopython, code, fungi, pretty data, python, sci-blogs, sunday spinelessness, taxonomy