The origin of Hox genes: a telltale neighbourhood

Gods, it’s been so hard to keep my mouth shut about this. A friend of mine just published a paper about Hox genes, and I’ve known about it for a while and it’s been keeping me crazy excited because it’s fascinating and, well: Hox genes! Now that it’s finally out, I can blather about it to my heart’s content, and so I will. Be prepared for a long ride 😉

First of all, a quick rundown of Hox genes for those who aren’t evo-devo geeks. These genes encode transcription factors – proteins that switch genes on/off. They are members of the large and distinguished class of homeobox genes, many of which play important roles in orchestrating embryonic development. Hox genes in particular are famous for laying out the plan for the head to tail axes of bilaterian animals, and for often sitting in neat clusters in the genome and being expressed along the body axis in the same order they are in the cluster. (Below: one of my favourite scientific figures ever, a fruit fly embryo stained in different colours for each of its Hox genes*. From Lemons and McGinnis [2006] via Pharyngula) In short, Hox genes are fucking awesome and extremely important to boot.

Tracing origins

One of the unresolved questions about Hox genes is exactly where they come from, and the new study draws some interesting conclusions regarding their origins. Before we delve into Mendivil Ramos et al. ( 2012) itself, perhaps it’s best to pull out my old sketch of animal phylogeny, because the relationships of the great old animal lineages are kind of important for the discussion. So this is the family tree of animals at first approximation (photos were all sourced from Wikimedia Commons; more info about them in my Nectocaris post):

Mendivil Ramos et al. follow one of the more popular resolutions of the question marks, in which cnidarians are closest to bilaterians and placozoans are the sister group to cnidarians+bilaterians. They don’t talk too much about ctenophores, but I’ll return to that later 🙂

Bilaterians all have Hox genes, and in most of them they do what they were originally discovered doing in fruit flies: patterning the anterior-posterior axis as they say in Jargonese. Some bilaterians have duplicated individual genes or even whole Hox clusters (we have four clusters, and salmon have as many as 13), but it’s pretty uncontroversial that a neat Hox cluster with representatives of most existing types of Hox genes was present already on the left side of the bilaterian box. So was the little sister of the Hox cluster, unimaginatively called the ParaHox cluster, which only contains three kinds of genes but operates in a similar way to its more famous sister (Brooke et al., 1998).

Where did Hox and ParaHox genes come from? Given the phylogeny of the genes, it’s likely that there was originally a small (maybe 2-3 genes) ProtoHox cluster that duplicated to give rise to both Hoxes and ParaHoxes. We know that cnidarians like sea anemones have both Hox and ParaHox genes, which behave somewhat like their bilaterian counterparts (Ryan et al., 2007). Therefore, the ProtoHox cluster must have existed before the common ancestor of these two great lineages.

Enter the Blob

What about placozoans? That’s where things get a bit complicated. Trichoplax, the mysterious little blob that is the only living representative of this oddball phylum, has only one Hox-like gene noncommittally named Trox-2. A relic of the ProtoHox era? Not really – in phylogenetic analyses of the protein sequence, it tends to group with the ParaHox gene Gsx, whereas you would expect a leftover ProtoHox gene to remain outside the Hox+ProtoHox clique.

Is Trox-2 a ProtoHox gene anyway? That would mean something weird happened in the evolution of Hox and ParaHox genes after the cluster duplication: Gsx (and its sisters Hox1-2) would have stagnated somewhere near its ancestral condition while all the other genes sped ahead. It’s a long shot, but evolution has been known to do strange things to gene sequences. Also, homeobox genes are often difficult to classify by sequence alone. Scientists typically use the DNA-binding region that the homeobox encodes for this purpose, but a homeodomain is only 60 amino acids and simply doesn’t contain enough information to place some problematic sequences. And unless we’re examining very closely related genes, the rest of the protein sequence is too different to be compared.

Guilt by association

However, there is another way of solving the mystery. Hox and ParaHox genes are not alone in the genome. They sit on huge chromosomes, and while they tend to banish non-*Hox genes from among them, the flanks of each cluster are populated by a variety of unrelated genes. The key thing is that Hox clusters and ParaHox clusters have different neighbours. Thus, looking at a problem gene’s neighbours can tell us what it is!

(Above: the neighbours of Trox-2. Yellow genes are ParaHox neighbours in humans, green genes are Hox neighbours, grey genes have no human counterparts, and orange genes are parts of both Hox and ParaHox neighbourhoods. From Mendivil Ramos et al. [2012])

This is exactly what happened. My lovely friend Olivia looked at the chunk of genomic sequence that contains Trox-2 and found about two dozen genes on it that had clear homologues in humans. She then tallied where each of the human homologues were, and behold: many of them crowded around ParaHox clusters (we also have several of those, courtesy of whole genome duplications), while only one was a Hox neighbour in humans. If Trox-2 were a ProtoHox, we’d expect a mixture of Hox and ParaHox neighbours, but that’s not what we find at all. Statistically speaking, it’s a no-brainer. Trox-2 is exactly where a ParaHox gene should be.

Ghosts in the genome

Now, we have a problem. If Trox-2 is a ParaHox gene, it must have come after the Hox/ParaHox duplication. So where the hell is the Hox cluster? Well, seeing as Trichoplax only has one ParaHox gene instead of the more typical three or so, gene loss certainly sounds like a possibility. Is there an “empty” Hox cluster lurking somewhere in the blob’s genome? Here, cnidarians turn out to be pretty helpful. After sequencing the genome of the sea anemone Nematostella vectensis, Putnam et al. (2007) attempted to reconstruct parts of the original chromosomes of the cnidarian-bilaterian ancestor. They called the results Putative Ancestral Linkage Groups, in other words, groups of genes that have stayed together since cnidarians and bilaterians diverged 600 or so million years ago.

One of these PALs contains over 200 conserved Hox neighbours, nearly all of which are present in Trichoplax. Strikingly, about half of them are close enough to one another that they are in the same chunk of sequence even though the Trichoplax genome hasn’t been stitched together to the level of whole chromosomes. That’s much more than you’d expect by chance. Trichoplax has a Hox locus without Hox genes, what Mendivil Ramos et al. call a ghost Hox locus.

Hox genes all the way down?

If you followed so far, you might have noticed that we’ve been pushing that elusive ProtoHox further and further back in animal evolution. It preceded bilaterians, it preceded cnidarians and bilaterians, and now it turns out it also preceded our split from placozoans. Will we find it if we look in the remaining animal lineages? Since a ctenophore genome hasn’t yet been released to the public, that question transforms into: will we find it in sponges?

The sponge Amphimedon queenslandica does have a publicly available genome, and much has been made of its apparent lack of many developmentally important transcription factor families (e.g. Larroux et al., 2008). It doesn’t have anything that looks like a Hox, ParaHox or ProtoHox gene, but what about the neighbourhoods?

Like that of Trichoplax, the Amphimedon genome sequence is in relatively small pieces, so a little clever statisticking was needed to decide whether it contains Hox, ParaHox or ProtoHox neighbourhoods. The starting points were the PAL of Hox neighbours mentioned above, and a PAL of ParaHox neighbours the team constructed using the human and Trichoplax genomes. These genes were distributed among many genomic scaffolds, but of course lacking chromosome-level information the group didn’t know whether any of these scaffolds are actually linked to each other in the sponge genome.

The solution was a simulation: take the number of genes in the PAL, take the number and size (in number of genes) of the thousands of Amphimedon scaffolds, and scatter the PAL members randomly among the scaffolds with the larger scaffolds proportionately more likely to receive a PAL gene. When all the PAL members are handed out, count the number of scaffolds with PAL members on them. Repeat this a thousand times, and you get an idea what the distribution of Hox and ParaHox neighbours would be if they weren’t clustered together. This approach showed that the real distribution is anything but random. Hox and ParaHox neighbours are clearly clustered in the sponge genome, and what’s more, they are clustered separately.

Still no ProtoHox locus, in other words. At some point in the murky depths of their ancestry, sponges lost bona fide Hox and ParaHox genes!

So…

That raises a couple of issues. First, where is the ProtoHox? Hox-like genes have never been found outside animals. These are smart people we’re talking about, so they checked the genome of the closest non-animal relative we have today, a choanoflagellate. Neither Hox/ParaHox nor ProtoHox neighbourhoods were there – the PAL genes didn’t cluster together any more than they would by chance. The whole *Hox phenomenon seems unique to animals (or else the choanoflagellate genome is totally scrambled). It appears that somewhere in our ancestry, ProtoHox gene(s) appeared and parted ways before sponges split from the rest of the animals. Since we have no surviving descendants of these ancestors outside of sponges and the rest of the animals, we’ll probably never find unduplicated descendants of the ProtoHox cluster.

Second, what happened in ctenophores? Everything we know about their genomes suggests that they completely lack Hox-like genes. Although there have been studies that placed them even further out than sponges (Dunn et al., 2008), it’s more likely that they are much closer to bilaterians than that (Philippe et al., 2011). I think I’m not the only one itching to examine a ctenophore genome for Hox neighbours…

And finally, if some distant ancestor of all animals had full-blown Hox and ParaHox clusters, what the heck was it doing with them? Was it something unexpectedly complex that would need genes for axial patterning? Are sponges and placozoans grossly simplified descendants of a much more complex ancestor, or did Hox-like genes only become involved in dividing up body axes later in evolution?

The more we learn the less we know. One thing is (once again) clear: assuming that a simple animal is a good proxy for an ancestral animal is a dangerous, dangerous assumption to make.

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*Technically, fruit flies have twelve Hox genes, but only seven are shown in the image. Hox2/proboscipedia is a normal Hox gene involved in the development of mouthparts among others, but four more genes have completely lost their “canonical” Hox gene-like activities. That includes all three of Drosophila‘s weird triplicated Hox3 genes.

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References

Brooke NM et al. (1998) The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature 392:920-922

Dunn CW et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 457:745-759

Larroux C et al. (2008) Genesis and expansion of metazoan transcription factor gene classes. Molecular Biology and Evolution 25:980-996

Lemons D and McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918-1922

Mendivil Ramos O et al. (2012) Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals. Current Biology in press, available online 26/09/2012, doi: 10.1016/j.cub.2012.08.023

Philippe H et al. (2011) Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biology 9:e1000602

Putnam NH et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317:86-94

Ryan JF et al. (2007) Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis. PLoS ONE 2:e153

Velvet worms in a prettier light

I bumped into Mayer et al. (2010) while hunting for reagents to use in an experiment I’m planning. The article is about segmentation (sort of), so I had to have a closer look, and man. Those pictures. Fluorescence and a good microscope can do wonders. This is what a velvet worm looks like in normal light (whole body shot of an unspecified peripatid by Geoff Gallice, Wikipedia, and portrait of Euperipatoides rowelli by András Keszei via EOL):

I think they are adorable and cuddly the way they are (apart from that hunting with slime bit), but they look simply gorgeous if you stick some glowing antibodies to them and start playing with a confocal ‘scope.

This is a fairly late-stage embryo of E. rowelli, the same guy waving its chubby leggies at you in the right-hand photo above. The green dots are cells that were copying their DNA when the baby was killed (all of the pictures below are from Mayer et al., of course):

These are younger embryos of the same species, with all their DNA labelled in blue and dividing cells labelled in red:

And these are embryos of another species from the same family as the unidentified guy from Wikipedia (colours are the same as above):

Seriously, there is something about the mystical glow of these images that always gets me. I think you could make almost anything look beautiful with a fluorescent marker and the right equipment. I know aesthetic appeal isn’t the primary aim of scientific imaging, but damn. Look at those alien creatures glowing with the light of the unknown.

In case you wondered, the point of the paper is that velvet worms lack a posterior growth zone. That means that when they develop their numerous segments, there isn’t a well-defined pool of cells at the rear of the embryo that divide to generate segment material. As you can see in all the red glow, cell division happens evenly all over the place. Why is this significant? Well, posterior growth zones were thought to be one of the characteristics that segmented animals might have inherited from their common ancestor. But Mayer and colleagues point out that the existence of a PGZ in the arthropod ancestor is dubious at best, and velvet worms (one of the closest living relatives of arthropods) also lack one, so maybe it’s kind of wrong to use the PGZ as an argument for the common ancestry of segmentation.

(There, that’s the science in a nutshell. Now I’ll just go back and admire the pretty glowy pictures some more :D)
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Reference:

Mayer G et al. (2010) Growth patterns in Onychophora (velvet worms): lack of a localised posterior proliferation zone. BMC Evolutionary Biology 10:339

More genes from scratch

Following on from the yeast “proto-gene” study, I’ve started paying more attention to news about gene birth from non-coding DNA. (Or “junk” DNA, if you will, though “junk” is… something of a misnomer :-P) The yeast paper explored protein-coding genes in the process of birth. This new one I found in PLoS Genetics looks at genes that have already been born, and argues that the sequences they came from were functional long before they began to serve as templates for proteins.

Paternity testing for genes

So how do you know that a protein-coding gene came from non-coding DNA? Xie et al. (2012) looked specifically for genes born along the ape lineage, that is, the group that includes gibbons, orangs, chimps, gorillas and ourselves. They searched for human genes that had no protein-coding homologue in non-apes including rhesus macaques, mice, dogs and a handful of other mammals, but did match some of the other animals’ DNA sequence. It was also important that there were no other similar sequences in the human genome itself, which might have indicated that the “new” gene actually originated by duplication.

To ascertain that the selected genes represented gene birth in the ape lineage as opposed to a dying gene in other mammals, they also looked at the sequence changes that garbled the would-be protein product of the non-ape sequences. If these are the same in all non-ape versions of a gene, that probably means that they were inherited from the common ancestor of apes and all these species, that is, the non-coding version of the gene came first. Only genes that really seemed to have been born in our lineage were kept.

In the end, they came up with 24 genes that passed all muster. Some of these coded for proteins in both chimps and humans, others only in humans. Based on RNA-sequencing data from rhesus macaques, 20 non-coding versions of these genes were active in monkeys – and this is where things get interesting.

Function in the junkyard

The big question the team asked was this: are these non-coding RNAs just random noise in transcription, or are they already functional even without a protein product? They decided to answer this question by looking at the structure and expression patterns of the RNAs in macaques, chimps and humans.

By “structure”, they mean how the RNA is edited after it’s transcribed from the gene sitting in the DNA. The RNA from most genes in animals and other eukaryotes isn’t taken straight through protein synthesis. First, pieces called introns are chopped out and the rest (called exons) are spliced together to yield the final template for the protein.* When the researchers looked at RNA sequencing results from the three primates, they found that the non-coding sequences in macaques were cut and joined at the same points that the protein-coding human sequences were: a bunch of RNA sequences from macaques spanned both sides of a human splice site, and contained none of the intron in between. Such conservation, the authors argue, is indicative of functionality.

Expression patterns also suggested that the macaque sequences weren’t just noise: when they compared the abundance of the different RNAs between different tissues in the three primates, Xie et al. found that the non-coding RNAs weren’t just expressed all over the place – they were significantly more abundant in some parts of the body than others. This pattern was consistent across species: a sequence that was most abundant in the macaque’s brain was also likely to be brain-specific in humans, even though the macaque version didn’t code for a protein and the human gene did. (By the way, a lot of the 24 were most active in the brain, which is apparently something of a trend among new human genes regardless of their mode of origin. Guess our brains evolved rather a lot in the last few million years ;))

This is very cool, but I’m kind of worried about the arguments used for functionality. Maybe this is just me being a newbie in this area, but I’m not sure that useless non-coding RNAs should be expressed all over the place. One of the salient features of the 24 genes in this study is that they are nearby other genes, sometimes even overlapping them. In any case, they are close enough to use the switches that normally regulate the activity of the other gene(s). That would mean that they’d be most highly expressed wherever their neighbours are, which doesn’t depend on them having a function. If some of them happened to acquire proteing coding potential by mutation, presumably it’d only be kept by natural selection if the resulting proteins did something useful in those places, hence the conservation of expression patterns.

Likewise, splice sites may well arise by accident (they aren’t all that complex), and they don’t have to disappear just because a mutation somewhere else makes the sequence suitable for protein synthesis. Though in fact, splice site conservation sounds more convincing than expression conservation to me as far as arguments for function go. Because splice sites can come and go quite easily, there’s no reason they should be particularly conserved between any two sequences unless they’re important. And the splice sites can only be important if the sequence they’re in does something. Who cares where you cut a strand of random RNA that’ll only end up eaten by housekeeping enzymes anyway?

So, while I get all excited about the whole new genes side of things, and I love this sort of genomic detective work, I think I still have to sleep on that point about function coming before protein. It’s a pity they didn’t check if any of the “non-coding” RNAs in macaques (and chimps) were occasionally translated into a protein, albeit a smaller one than the human counterpart. The yeast people did that and it was awesome, and it would have been such an informative thing to do in this case.

(Also, it would have been darn cool if they’d tried knocking out some of them and seeing if they got screwed up monkeys, but let’s be realistic. Macaques don’t breed like mice, they take a hell of a long time to grow up, and we’re kinda reluctant to mistreat our close relatives like that. You’d have to be comic book supervillain insane to embark on that experiment.)

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*This may sound like a weird way to run a genome, but it’s actually quite good for making more than one product from the same gene. It’s pretty important in real life – nearly all human genes with multiple exons are spliced in at least two different ways, and many genetic diseases originate from messed up splicing.

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Reference:

Xie C et al. (2012) Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genetics 8:e1002942

Animals, amoebae and assumptions

Animals aren’t the only multicellular creatures in their phylogenetic neighbourhood. Social amoebae, many fungi and quite a few of the poorly known choanoflagellates spend at least part of their lives as collections of cooperating cells. Conventional wisdom has been that these groups invented multicellularity independently, but maybe conventional wisdom needs a bit of challenging.

To tell you the truth, I never really thought about the other possibility, that being multicellular is the original state of affair for these organisms. I never really considered the evidence on which the conventional wisdom was based. You could say I didn’t really care either way. A while back I saw a paper that said something about a social amoeba having an epithelium, but I just kind of shrugged and went on with my life. I don’t know, now an article in BioEssays brought this up again, and I’m not sure I was right to ignore it back then. I think Dickinson et al. (2012) have a point, and I think some assumptions may need to be reexamined.

In case you wondered, an epithelium is a type of tissue made of a layer or layers of polarised cells. “Polarised” means that various cellular components – proteins, attachments to neighbouring cells, organelles – are distributed unevenly in the cell, clustered towards one or the other side of the cell layer. Epithelia line pretty much everything in a typical animal’s body, from, well, the entire body, to things like guts and glands. They secrete important stuff like hormones, and their closely packed cells form a barrier to keep molecules and pathogens where they belong. An epithelium was thought to be a uniquely animal thing to have, but looking more closely at that weird little amoeba suggested it may not be.

The paper that I ignored was Dickinson et al. (2011) – yes, by the exact same people who wrote the BioEssays piece. OK, I didn’t completely ignore it. I read enough of it to scribble a quick note in my citation manager saying “screams convergent evolution to me”. The paper examined the multicellular stage in the life of Dictyostelium discoideum, an ordinarily single-celled amoeba that reacts to food shortages by crowding together with friends and family to form a fruiting body that helps disperse some of its cells in search of new habitats. The fruiting body is pretty complex for a “unicellular” creature, and it turns out that this complexity includes a region of tissue that looks quite a lot like a simple epithelium. It doesn’t just look like one; it sorts out its insides and outsides with the help of proteins called catenins, which are also involved in cell polarity in the epithelia of animals. (Below: D. discoideum being multicellular, from Wikipedia)

That isn’t much evidence to base an inference of homology on, especially since other key players in animal cell polarity are entirely absent from D. discoideum. But equally, the fact that tons of unikonts (the group including amoebae, slime moulds, fungi, choanoflagellates and animals) are single-celled doesn’t mean that the multicellular groups all came up with the idea independently. Evolution doesn’t always increase complexity – sometimes complexity becomes superfluous.

I remember when we discussed the choanoflagellate genome paper (King et al., 2008) in class. The genome in question belongs to a purportedly single-celled creature, but it contains tons of genes you’d think only multicellular organisms would need, such as genes for cell-to-cell adhesion proteins. So one explanation is that these proteins originally did something else, like anchoring a single cell to its favourite spot. Another explanation is that they did have something to do with multicellularity – it just wasn’t the multicellularity of animals at first.

This suggestion isn’t terribly controversial when you’re talking about choanoflagellates, since some of them do obviously form colonies (one such colony of Salpingoeca/Proterospongia rosetta is shown below, from Mark Dayel of the King lab via ChoanoWiki). It’s not hard to imagine that either the “single-celled” species whose genome was sequenced also has a colonial stage the scientists just never saw, or that its recent ancestors did.

Whether or not the same applies to the whole of unikonts is a more difficult question. I’m not at all familiar with the details of unikont relationships, but based on the tree shown in the BioEssays article, multicellularity is all over the group. In most cases, it’s facultative multicellularity; animals are rather the exception in being doomed to it for their entire lives. However, if you just looked at that tree, you’d wonder why the hell anyone thought the common ancestor of these things wasn’t some kind of multicellular.

Yet the details of animal-like multicellularity aren’t so widespread. True cadherins (the cell adhesion proteins I mentioned) have only been found in animals proper. Choanoflagellates and some even more obscure relatives of animals have bits and pieces of them, and other unikonts have none at all as far as anyone knows. Epithelium-like tissues have only been described in that one species of amoeba – but, as Dickinson and colleagues note, no one really looked in the others.

Personally, I wouldn’t be at all surprised if the conventional wisdom ended up shifting. I still don’t think that the evidence from Dictyostelium is enough to draw a conclusion. We obviously need to know a lot more about unikont genomes, tissues and life cycles to piece together the history of multicellularity in the group, but I’m not sure that right now a unicellular ancestor has a lot more going in its favour than a multicellular one. Guess we’ll have to wait and look with an open mind 🙂

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References

Dickinson DJ et al. (2011) A polarized epithelium organized by β- and α-catenin predates cadherin and metazoan origins. Science 331:1336-1339

Dickinson DJ et al. (2012) An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity. BioEssays advance online publication, 29/08/2012, doi:10.1002/bies.201100187

King N et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788

 

Hourglasses everywhere

Ever since the theory of evolution “evolved” centuries ago, scientists have known that evolution and development are somehow related. In his Origin of Species, Charles Darwin devoted pages to the discussion of this relationship. Ill-fated theories like Haeckel’s infamous biogenetic law aside, the idea is still alive and well – in fact, it’s the foundation for the discipline of evolutionary developmental biology or evo-devo. (Yay!)

Now, the fact that embryos of related (or even seemingly unrelated) animals are often more similar than their adults has been known for a long time. But exactly what pattern these similarities follow throughout embryogenesis is a slightly more contentious issue. You might expect that embryos would start out more similar and accumulate differences as they grow into their different adult forms. But, at least for some well-studied animal groups including vertebrates, that doesn’t seem to be the case. Instead, the embryos start out pretty different, then become more similar until they reach a point of maximum resemblance (called the phylotypic stage, where the characteristic body plan of the phylum is established), and finally begin to diverge again.

(Below: two competing views of developmental evolution. Image from Irie and Kuratani (2011) via PhysOrg.

 

The original debate over whether phylotypic stages existed involved only the morphology of the embryos, but nowadays, everyone is sequencing everything, and the funnel vs. hourglass debate also moved on to a molecular level. About a couple of years ago, two papers in the same issue of Nature reported the discovery of the hourglass in the transcriptomes – the set of active genes – of two very different kinds of animals.

Kalinka et al. (2010) showed that the embryos of six fruit fly species activate the most similar set of genes at the same developmental stage where arthropod embryos in general look most similar to one another. Using a different approach, Domazet-Lošo and Tautz (2010) determined that zebrafish embryos express the oldest genes at the (vertebrate) phylotypic stage. Genes that only evolved recently are mainly active in the earliest and latest stages of development, and sexually active adults express the youngest genes. (For a proper discussion of these studies, head over to The Panda’s Thumb for Steve Matheson’s lovely posts on them.)

Thus, genes offer an independent line of evidence for the existence of the embryonic hourglass. If the embryos themselves didn’t give a clear answer, perhaps two different kinds of genetic evidence offer a more persuasive argument. Not to mention that the evidence just keeps piling up. Irie and Kuratani (2011) compared gene expression in embryos of four distantly related vertebrate species, which is a direct comparison across ten times more evolutionary time than the fly study – and once again, the hourglass was there, with its waist sitting right at the traditional phylotypic stage. Clearly, there is something about this stage that acts to preserve it over hundreds of millions of years of evolution in animals with wildly different lifestyles and reproductive habits.

And, perhaps, there is something about the phylotypic stage that compels it to evolve again and again. The most recent “transcriptomic hourglass” study isn’t about animals at all – it’s about plants. As far as anyone knows, plants evolved multicellularity and embryos completely independently of animals. Yet here’s an unassuming little plant, the plant geneticists’ workhorse Arabidopsis thaliana, with a beautiful transcriptomic hourglass eerily like that of the animals.

(Below: Arabidopsis not looking like the most important plant in science, from Wikipedia.)

Quint et al. (2012) more or less did the same thing Domazet-Lošo and Tautz did with their zebrafish, calculating the age of the genes expressed at seven different developmental stages in baby Arabidopsis. They also estimated how fast each gene evolved by comparing their sequences to some close relatives of A. thaliana. They found that the oldest and most conservative genes were expressed somewhere in mid-embryogenesis. It was undoubtedly an hourglass.

The result is all the more interesting because plants don’t have an obvious developmental hourglass in terms of morphology. Quint and colleagues observe that different land plants don’t actually differ all that much as embryos, and the divergence of their adult appearances begins well after the waist of the transcriptomic hourglass. What’s going on here? Do animals and plants have transcriptomic hourglasses for different reasons? The authors of the plant paper also note that in both animals and plants, it’s mostly the young genes that account for the transcriptome age variation throughout development. The old genes are on from start to finish. On top of them, one set of young genes is activated early on, then they are switched off and you’re left with the old “phylotypic transcriptome”, then another set of young genes is turned on. That would indicate that the hourglass is really something plants and animals have in common, but I think a lot more embryos must grow into adults before someone figures out exactly what this means…

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References

Domazet-Lošo T & Tautz D (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468:815-818

Irei N & Kuratani S (2011) Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nature Communications 2:248

Kalinka AT et al. (2010) Gene expression divergence recapitulates the developmental hourglass model. Nature 468:811-814

Quint M et al. (2012) A transcriptomic hourglass in plant embryogenesis. Nature advance online publication 05/09/2012, doi:10.1038/nature11394