Springwatch

I hope you caught the first episode of the 2011 BBC Springwatch season. Whilst watching, it struck me that the film and photography featured is going to be a fantastic resource for biologists to come. As scientists become ever more aware of the importance of context and as we wish to study behaviour and the dynamic properties of organisms, the action of live organisms is increasingly a point of study. When thinking like this, video like that on Springwatch is equivalent to the data preserved in museum collections (containing preserved individuals and associated information): data which we use to understand the species and groups the specimens or film represents. These recordings are specimens, just like anything in a museum cabinet.

All collections need curation and the BBC (in addition to all of the education, programme-making etc.) curates a HUGE collection of wildlife film, certainly no small task! Worth the license fee? Absolutely!

Queen of the flies

Bees are cool. Supersocieties, domestication, the waggle dance and delicious sweet honey. And now this: Royalactin induces queen differentiation in honeybees.

For a long time, the existence of 'castes' (worker, queen, soldier etc.) in social insects has been a subject of much thought by biologists. Clearly all members of a  hive have the same genome, so the fact that individuals have such varied appearance (and that this is very predictable - all workers are more or less identical, but very different from queens etc.) is a compelling argument for the primacy of environmental factors in development. The difference between workers and queens is obviously not genetic (in the bases of the DNA itself) but turns out to be epigenetic. The DNA in the nucleus of a cell is wrapped around proteins called histones. These histones can be modified by other enzymes which affects the interactions between neighbouring histones and alters the level of activity of  nearby genes by altering the accessibility of particular DNA residues.

All female bee larvae are 'born' equal (there is no difference between worker and queen embryos - they are equivalent). What determines the developmental trajectory of a young bee larva is the amount of royal jelly it is fed. Something in the royal jelly produced by worker bees causes the histones to be altered differently in worker and queen embryos, leading to differences in gene expression, leading to changes in development leading to very different adult forms.

The paper this week from Masaki Kamakura goes looking for what exactly it is in the royal jelly that has this queen-making potential. By very carefully analysing royal jelly, by testing its components individually for the ability to evoke 'royal' changes (such as increased growth and larger ovaries), it is possible to demonstrate that the action of royal jelly is due to a previously described protein named royalactin. Obviously, this is an interesting finding, but to corroborate royalactin as the crucial factor, we would like to know something about the mechanism by which its ingestion can bring about the profound developmental changes necessary to produce a queen bee rather than a worker.

Kamakura does this by making queen flies.

The fruit fly Drosophila melanogaster is a model organism for many biological processes and is here used as a perfect model of bee development. When Drosophila larvae were fed on a diet of 20% royal jelly in addition to their normal food, the adult flies showed many similarities with queen bees (quicker development, larger size, higher egg production and a longer life). The picture at the top of this post is from the paper. The fly on the left is a normal female, whereas the fly on the right was fed on the 20% royal jelly diet, clearly showing the increased size.

Kamakura examines the effects of feeding some mutant strains of Drosophila the royal jelly diet. Flies with defects in the Egfr signalling pathway do not show the 'queen fly' effect, suggesting that royalactin acts via this pathway. He also engineered flies to express royalactin themselves and demonstrates once again that this protein can cause the queen fly effect and that the Egfr pathway seems to be involved. Finally, Kamakura knocks out the EGFR pathway in developing bees using a technique called RNA-interference and shows that when EGFR signalling is inactivated, individuals fed royal jelly do not develop perfectly as queens.

This is a very interesting piece of work, thoroughly deserving of a place in Nature. We can see the conservation of signalling systems between bees and flies and can imagine how caste differentiation in bees could have evolved - existing developmental pathways are subtly modified to give a new phenotype. The ability of one genome to produce multiple alternative forms in different contexts is conclusive proof of the importance of developmental plasticity both in the short-term (development of indivduals) and on a much larger evolutionary scale (in the appearance of new features and traits).

Mendeley

To organise my collection of papers and references I use the reference manager Mendeley.

Mendeley is a desktop application (very similar to Mekentosj Papers in this respect), a cloud-based community for backup, storage and sharing of papers and a scientific social network (a bit facebook, a bit LinkedIn).

The desktop application curates your collection of pdfs:

The panel on the top left contains your list of folders and public groups (see below for more on these), the bottom left panel enables you to search by author, author's keywords, journal or personal tags in your tag-cloud. The middle panel displays the documents in whatever folde is open and the right panel shows the metadata for the selected paper (title, author, tags, abstract etc.). Clicking on the pdf symbol next to a reference opens the reading screen:

Here you have the option to read fullscreen, as well as edit metadata on the right as well as highlight and annotate the paper itself (very handy!). Mendeley tabs all the references you may have open at any one time, making it simple to flip between them.

Importing papers is simple. You can either drag a pdf into your libary or select the 'Add Documents' button in the library screen. Mendeley then adds the pdf to your library, checks for metadata and automatically fills out Title, author, publication etc. This isn't perfect but it nearly always works and is improving - it's simple enough to edit incorrect entries: Mendeley lets you search Google Scholar with the title to fill out these fields if it can't find the reference in its catalogue. Best of all, Mendeley copies the pdf into a folder in its area of your hardrive and renames it in a format of your choosing: 'j.1365-294X.2011.05127.pdf' now becomes 'Legrand et al 2011 Molecular Ecology.pdf' for instance. These are stored in nested folders with a structure of your choosing.

This is all fantastic, and the cross-platform nature (there are Windows, OS X and Linux versions of Mendeley Desktop as well as iPhone and iPad apps to read your papers on the move) beats all competition hands-down, but Mendeley really comes into its own with its use of the cloud. Firstly, Mendeley allows you to sync your files between multiple computers - just click 'Sync' in the desktop app and all your references are downloaded. Amazing - no more carting around an external hard drive full of pdfs so you can work at home.

Mendeley is also great for collaboration: you can search for other users by email address and add your colleagues. You can then make groups or shared folders of references (complete with a facebook-like wall for discussion) with your collaborators. I use this feature to help run our journal club - it works brilliantly!

Finally, you can make a public profile to go with your Mendeley web presence:

Neat. This will make it easier for my colleagues to find me and share references.

Mendeley also does citation management. You can either export folders as Bibtex lists, copy and paste individual citations from the software itself, or install the plugin for Microsoft Word or Open Office. This lasst option is so easy to use its unreal. In Word:

Alt+M brings up a dialogue box where you can search your library

Select the appropriate reference and it is added. When you've finished the document, use the insert bibliography option in Word:

Very cool. The reference style is customizable too. 

These three bits of technology: Geneious, Google Reader and Mendeley save me HOURS of time and countless headaches and mean I sometimes actually enjoy working at a computer. No mean feat.

Computery things II - Google reader

Second on my list of things that make my life immeasurably easier (and hopefully help me be a better scientist) is Google reader.

For those that don't know, reader brings together all those dozens of websites, blogs and news feeds you check every day and collects them in one place. I have it as my homepage and I can easily skip through abstracts from the latest issues of Nature, Science, PNAS etc. as well as blogs. You can 'like' certain posts or star them for later (Google saves these in a special starred list) and clicking on the title of a post takes you to the corresponding website proper.

One particularly neat feature is the 'Explore' tab which displays new content from feeds related to stuff you already subscribe to. This a fantastic place to come across new feeds (I've lost count of the number of blogs and relevant journal articles I've found this way) and is a great way to kill some time and read something interesting without having to surf all over the place. Use this and people will think you're clever when in reality you're just poking around your homepage.

But what do you do with all the articles you find? The answer is MENDELEY.

Geneious

My apologies if this is only interesting to a narrow audience, but I would like to share my experiences of some software I’ve become a fan of. First off, Geneious.

Geneious is designed as an all-in-one bioinformatics application “that is both ultra-powerful and easy to use” (Geneious website). I first came across the free version years ago, but without any need for it at that stage, I didn’t pay too much attention. During my Master’s course at the NHM, I very suddenly became aware of the computing requirement for biosystematics.

Much of the work of our lab (pretty much all of it, to be honest) is in the comparative analyses of DNA sequences from bunches of related organisms, looking for hints of shared evolutionary history to make evolutionary trees and to estimate population genetics parameters and look for signatures of particular evolutionary processes. On a day-to-day level, what this means is lots of PCR in the lab followed by sequencing, the editing of sequences, the compilation of sequences into related lists (alignments) and the computational analysis of these alignments. The way things used to be set up meant that each step in this process used a different piece of software. Predictably, this was a bit of a nightmare. We would use one application to examine the raw sequence and edit obvious errors, followed by exporting it, then importing into a different program to do the alignment, then a third program to view and check the alignment (when you might have to go back to the first one to double-check) followed by analysis in a fourth or even fifth program! Each step has its own quirks (some software likes to disagree on standardized file formats, for example) and some bits only run on macs or pcs, or only have a limited number of licenses…. Nightmare.

This was when I tried the 14 day demo of Geneious Pro. I was sold. Now it was one application for everything. It would run on macs and pcs. It could search Genbank and download sequences for you. If you change one file, it can automatically update others documents that use that file. It can handle pretty sizable datasets (big chunks of genome).

It is quickly clear that it has been designed to be as user-friendly as possible. Every change you make is flagged, making it possible to see the editing history of a file and undo catastrophic mistakes. I wouldn’t go so far as to say it’s bulletproof (you can certainly do stupid things with it if you want), but its much more foolhardy than the alternatives.

I have only been using Geneious for about 6 months, but it’s already indispensable. With the trend towards ever more data (particularly with next-generation sequencing), the case for such an integrated, user-friendly and transparent piece of software becomes clearer and clearer.

The importance of museums

Aren't museums just spaces full of collecting things, organised neatly into categories and stored in their boxes? Aren't museums just tourist attractions?

NO! Museums are research institutions, educational facilities and incredible international resources as well as serving their obvious role in public engagement.

I am lucky enough to be studying at the Natural History Museum in London and I'm aware that many people aren't even aware that any science at all takes place there: "isn't that the dinosaur museum?!" The opening of the Darwin Centre aimed to make the museum's science a more integral part of the public offer, and seems to be succeeding (but there is still a long way to go yet).

So why do we have museums? Why is it that the government funds such institutions? What is their role?

The NHM's primary role is as a store of one of the most important collections of biological and geological specimens in the world.

These collections are not static either! They are sources of vital information about the diversity of living things, their relationships and characteristics. We can use them for morphological data, sources of DNA (the museum also maintains a collection of frozen DNA) and the maintenance and curation of collections is critical for the work of taxonomy (the naming of living things) as all species must be represented by a particular 'type' specimen which must be deposited in a museum to allow study by scientists.

What do we do all day?

[Picture: NHM]

I thought I should talk a little bit about the kind of work we do at the NHM. The research group I'm in is primarily interested in examining the evolutionary relationships among different lineages and species of beetles using DNA sequences (a pretty daunting feat given that about 25% of all species in the world are beetles) and the evolutionary and ecological forces responsible for beetle diversity. Secondary to all of the beetle work, the lab also works on some similar questions in flies and also the Papilio dardanus project which I work on, looking at the evolutionary biology of Batesian mimicry in this species.

The study of biological relationships (systematics) has been a core part of the museum's work since it's beginning and is intimately tied with the process of assigning names to species and higher groups (the discipline of taxonomy). Ever since Charles Darwin wrote the Origin, biologists have been interested in learning how the diversity of life forms we see today arose. Classically, organisms were grouped on the bases of shared characteristics, such as all mammals having hair and producing milk, with the groups assembled at a higher level using the discretion of the scientist. Such methods persisted for a long time, but were very subjective.

The arrival of computer power made it possible to be much more systematic in approach. Now, the possession of suites of traits could be coded numerically for all the organisms under study and the most parsimonious (simplest) evolutionary tree which would explain the data could be calculated. These methods are very powerful and made it possible to infer the relationships among large numbers of species and, critically, higher-level groups such as genera or families. These methods are still used today, particularly when fossil taxa are being examined - their morphological characters can be coded as for any existing species.

The second revolution in systematics is the use of DNA sequencing. Now, all subjectivity in character coding is removed and the DNA sequences can be analysed to give the evolutionary tree. This is far from straightforward and requires the use of very sophisticated mathematical models of DNA sequence evolution and large amounts of computing power. This technique has been enormously successful and is especially useful when dealing with problematic animals (such as insects) where it can be very difficult to distinguish one species from another on morphology alone and large numbers of species remain undescribed. These are the methods our group uses at the museum for our work.

New advances in technology mean that it is becoming easier and easier to get sequences from more and more genes from more and more species and with increasing computer power, ever more complicated models can be used to infer the most likely evolutionary tree. With a growing number of species having completely sequenced genomes, the next revolution in systematics - phylogenomics - may be just around the corner. This is a very exciting time to be in a molecular systematics lab.

Four new species of lizard, made in the lab

This is so cool! Laboratory synthesis of an independently reproducing vertebrate species. This might take some explaining, so bear with me (it's worth it!)

Firstly, an introduction to chromosome numbers ('ploidy').  You and I have two copies of each of 23 chromosome - we say we are DIploid. Gametes (sex cells - sperm and eggs) usually have one copy of each  chromosome; they are HAPloid.

Now, out in the deserts of New Mexico, there are some species of lizard that reproduce parthenogenetically. This means that the females produce genetically identical copies (clones) of themselves. These lizard populations are all female and there is no sex. These lizards with a bizarre reproductive strategy are the result of hybridisation between two sexual species. Many (5 of 7) of these species are TRIploid: they have 3 copies of each chromosome. These triploid species are thought to have arisen through hybridisation (a single mating) between a male from a sexual species and a female of a diploid, parthenogenetic species.

Normally, offspring from crosses between different species are sterile (e.g the mule - a horse x donkey cross), so the fact that these offspring can reproduce is weird enough, especially since it has happened so many times and involves the total loss of males and sex, but what happens next is absolutely unprecedented and astounding. The authors of this paper crossed diploid males with one of the triploid, female only species (although these don't ordinarily have sex, the females are still capable). The result is a TETRAploid lizard (four copies of each chromosome) which can reproduce parthenogenetically and is isolated from both parent species. This was repeated to produce 4 lineages. Voila! Instant new species, made in a laboratory!

Life really is stranger than fiction.

Sex mosaics

This is a sex mosaic ('mosaic gynandromorph') Papilio dardanus from our breeding experiments last summer. The left wing is mostly the pattern of the female form cenea, but the right wing shows lots of yellow patches of male pigment. There is even a segment at the bottom corner with male patterning and even a little bit of a tail.

It is thought that this kind of pattern arises (in Lepidoptera at least) from the loss of one of the female-specific sex chromosome from one of the two daughters of a cell division. In butterflies and moths, the sex determination system is the other way around to humans - males have two identical sex chromosomes (ZZ rather than XY) and it is the females with two different sex chromosomes (ZW contrasting with XX in humans). If this loss happens very early in development whilst the embryo is only a few cells, the result can be a striking bilateral gynandromorph:

[Papilio dardanus bilateral gynandromorph - left side female form cenea, right hand male]

However, if the error occurs later in development, the result will be a mosaic as in the first picture. Isn't biology cool?!

Moths moths moths

Following on from yesterday's post about the peppered moth we have Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin.

This paper follows on from the failure to pinpoint any of the usual suspects as responsible for the two alternative forms of this moth, mottled or black. By examining the offspring of matings between the two forms, the authors were able to home in on the region responsible. This DNA of this region was then sequenced and compared with the genome of the silkmoth. They found that this region corresponds to part of chromosome 17 in the silkmoth and the order of the genes along the chromosome is the same in both species. With some sequences of these genes in hand, the authors could now examine the differences between the two  forms of peppered moth more closely.

Moths were collected from across the UK for DNA analysis using 6 sites along the chromosome region suggested by genetics. The authors found that some of these sites showed statistically significant association with the wing pattern (peppered or dark). Because of the strong similarity of DNA sequences from the darker moths (compared to the much higher diversity among the typically patterned moths), the authors suggest that this form only arose once in Britain.

Having demonstrated that one region in particular is associated with the darker pattern, and that this darker pattern arose once, the next question is to look for a genetic cause, particularly in light of the failure of the candidate gene approach. By looking at the statistical associations among DNA sequence variants, it was possible to narrow the chromosomal region of interest to about 200,000 nucleotides (the 'letters' of DNA - A, T, G and C). This region is the peppered moth equivalent of a chromosomal region known to be important in butterfly wing patterning - the Bigeye region in the African butterfly Bicyclus anynana and a region known to be important in determining elements of the wing pattern in South American Heliconius butterflies.

These findings, together with the enormous amount of previous work on the peppered moth means that we can truly call this an icon of evolution: this one species of moth can tell us an almost unparalleled story about evolution. This is particularly relevant in the current context of climate change - the darker form of this moth arose once by a change in a genome region already known to be important in generating diversity in Lepidopteran wing patterns.

Icon of evolution

A two-parter playing straight to my interests. Firstly, from last year, Industrial Melanism in the Peppered Moth Is Not Associated with Genetic Variation in Canonical Melanisation Gene Candidates from Ilik Saccheri and Arjen van't Hof. Work on an iconic evolutionary system, a possible role for a developmental switch between alternatives, in a Lepidopteran no less and from Liverpool as well! All the boxes ticked!

The authors initially look at all the usual suspects for melanic (darkened) phenotypes; the genes encoding tyrosine hydroxylase, ebony, tan, yellows etc. using targeted PCR (looking to selectively amplify and sequence genes of interest by hoping that the sequence is sufficiently similar to that from previously studied species) and from sequencing particular expressed genes (PCR and sequencing messenger RNAs by a technique called 3` RACE).

They find that NONE of the usual suspects appear to be involved (unless they have also been duplicated and the second copy has undergone unprecedented sequence change): none of the genes involved show association with either the normal or the darkened forms.

So what is going on? It appears that none of the identified candidates are involved. It could be that a copy of one of the candidates has escaped undetected (most likely in the large family of yellow genes), but this is quite unlikely. It seems that the melanisation in the iconic peppered moth is underlain by changes in a previously unsuspected gene - perhaps a regulatory gene, such as a transcription factor, which directs the patterning and the levels of expression of melanisation genes in the developing wing discs. The alternative forms (alleles) of such a gene would underpin a switch between two alternative developmental paths - one leading to a 'peppered' moth and the other to a darkened form better disguised against soot-darkened trees. Natural selection by predators acting on conspicuous moths would have added a new switch to the developmental 'programme' of these moths.

More on this tomorrow....

Treehoppers

This is right up my street - evolutionary origin of morphological novelty by modification of a core developmental switch:

Body plan innovation in treehoppers through the evolution of an extra wing-like appendage

This article is a perfect demonstration of the power of evo-devo biology: how a previously enigmatic structure can be re-interpreted with knowledge of developmental genetics to give a profound and elegant explanation. The morphological novelty at issue here is the 'helmet' of treehoppers. Previous thought to be modifications of dorsal sclerites on the first thoracic segement (like the horns of rhinoceros beetles - see http://goo.gl/n3Oxz for a fascinating  new look at beetle horn development using ESTs and microarrays), this paper demonstrates evidence that the helmet is in fact an appendage of the first thoracic segment (because of the presence of jointed articulations between the body and the helmet).

Whilst ancient fossil insects have been interpreted as having T1 appendages, in all modern insects only the second and third thoracic segments in insects bear paired appendages in the form of wings. The authors demonstrate in this paper that the  dorsal appendages of all 3 segments (wings and helmet) show similar expression of the gene nubbin, conclusively demonstrating the homology of the wings and the helmet.

The authors suggest that the novel structure (helmet) has arisen due to an escape from repression of Scr by dorsal appendage genes including nubbin; treehopper Scr is still capable of repressing nubbin in flies. If this is true, it is a fantastic demonstration of the importance of simple regulatory changes leading to profound morphological change. Another very fine paper by the Prud'homme/ Gompel lab.

Context

I am obsessed with the idea of CONTEXT - how we cannot understand anything unless we also look at the context in whicch this happens. In biology, the importance of context is obvious. How a cell or an individual responds to a stimulus is entirely dependent on its context - what state it is in when the signal is recieved, what has happened to it in the past and what else is occuring at the same time. This spans behaviour, learning, cell biology, development, evolution, ecology etc.

This has an impact on my assessment of the (spurious) 'nature vs. nurture' debate. The 'nature' part (the genome) has zero adaptive value in its own right and it is only when it is expressed (which depends entirely on induction from external cues, be they truly environmental or from within the organism) that genetics can have any effect. Context (the entire extra-genomic part of an organism - all parts of the internal and external environment) is critical. Of course, genetic differences can alter the responses to cues and are the mechanism of transgenerational inheritance, but I think one needs to be very careful to avoid thinking in an overly deterministic way about biology.