The Mammal’s very own Hox genes (excite! Woo!)

It’s kind of hard to begin this post. First of all, let’s get the important news out of the way: I’ve just published a paper. In a moment, I’ll get around to discussing it at even more than my usual length, but I feel that I can’t do my excited puppy act without at least trying to capture how bloody much this paper means to me. The following may get a little personal; if you want to jump straight to the Cool Stuff, feel free to scroll a couple of paragraphs down.

<personal bit>

As you may have guessed from the long silence here, it’s not been a good handful of years, Real Life and mental health-wise. After my PhD, the prospect of the research career I’d dreamed of since I first began to grasp the meaning of the word “scientist” no longer seemed so dreamlike. It may surprise you to hear this from someone who finished a PhD with four published papers and spent the years of said PhD blathering regularly on the internet, but I find writing things for other people to read very, very stressful. In the case of a job application or a thesis chapter, that becomes “I’m not eating or sleeping properly” stressful. (Don’t ask me how I survived 20+ years of formal education.)

Long story short, for the last 3 years I’ve been getting by with a minimum wage job for which I’m both vastly overqualified and singularly ill-suited. I started the research project that culminated in the paper you can now read (for free, yay!) in BMC Evolutionary Biology (Szabó and Ferrier, 2018) while unemployed and broke, and I did most of it in my free time around work. This paper is a hard-won victory over myself and my circumstances. It’s a tiny glint of self-worth in the depth of the tunnel. In some ways, it was harder than my thesis: no funding body to satisfy, no lab mates to gripe at, no deadlines to spur me on. The only constant was my ex-supervisor turned co-author, who took my hobby project under his wings for the slim reward of having his name on a paper and nudged me into finishing it with unending patience. Here’s to Dave Ferrier, champion of non-model organisms, homeobox guy extraordinaire and all-round excellent human being. Dave, I hope you know you’re an absolute star.

</personal bit>

With that out of the way, it’s time for the Cool Stuff. There are Hox genes! More Hox genes than anyone ever imagined! (That is kind of the point, in fact!)

Apologies for the word count. I thought it would be a good idea to explain a few things, but also, I think I enjoy waffling about my baby far too much 😊

Hox therapy

The story of my Hox paper begins with an unemployed biologist with an overabundance of free time and a desperate need to do something scientific. Since I have a slightly odd idea of “fun”, back in 2015 I decided to catalogue Hox gene (or rather, protein) diversity in the animal kingdom, with particular focus on obscure and poorly studied groups. (I didn’t get very far, as we’ll see.)

Since it’s hard to discuss the paper without dropping some arcane zoological nomenclature, here’s my trusty old animal phylogeny to (re)acquaint us with the general outlines of the animal kingdom (I might need to update this in light of the Great Ctenophore Controversy some day, but we’re not dealing with anything outside the Bilateria today):

animalPhylogeny

For the purposes of my paper, we’re zooming into the deuterostome branch, which looks something like this on the inside (borrowing my own rather lacklustre last-minute figure from Szabó and Ferrier [2018]):

12862_2018_1307_Fig1_HTML

Everything on this tree apart from chordates (that’s us) belongs to a group called Ambulacraria, which contains two phyla, hemichordates (top two branches) and echinoderms (the next five). Echinoderms are the more familiar of the two – starfish and sea urchins and suchlike – and also the focus of my project. (I could find no Hox gene data from pterobranchs, which puts a slight caveat on everything I say about hemichordates)

Back to Hox genes.

Hox genes were kind of my gateway drug into evolutionary developmental biology. A few decades earlier, they had served the same purpose for developmental biology as a whole, since they were among the first genes to be discovered that (1) directed embryonic development (2) were comparable between very disparate animal groups. The short version, which will suffice for our purposes here, is that Hox genes are important in what we eggheads call anteroposterior patterning, or determining what body parts go where along the head (anterior) to tail (posterior) axis of a (bilaterian) animal.

In (I think, I haven’t counted) the majority of animals that have them, Hox genes are clustered to a greater or lesser extent. Rather than being scattered haphazardly across the genome, they sit close to one another along the same stretch of DNA. (Duboule [2007] is an excellent – albeit now slightly out of date – review of the various known configurations.)

Since my study is about echinoderms, the schematic Hox cluster shown below is the neatest known example from an echinoderm, the crown-of-thorns starfish Acanthaster planci (source: Baughman et al., 2014):

baughman2014_1

In this image, Hox genes are colour-coded according to a commonly used classification scheme. This classification is mostly based on the homeodomain, or the “business” end of the protein that a Hox gene encodes. A homeodomain makes up a relatively small portion (maybe 1/5th on average) of a typical Hox protein, but it’s the part that interacts with the DNA switches through which Hoxes control their target genes, and it’s often the only part that is similar enough to be compared between different Hox types.

The important genes for us today are the “posterior” Hox genes shown in pink and red above, especially the last two. The four posterior Hox genes seen here represent the “standard” set for ambulacrarians, although it’s uncertain whether Hox11/13b-c were already separate genes or just a single precursor gene in the ambulacrarian ancestor.

Eureka… or WTF?

“The most exciting phrase to hear in science, the one that heralds new discoveries, is not Eureka! (I found it!) but rather, ‘hmm… that’s funny…”Almost certainly not Isaac Asimov

In creating my grand catalogue, I’d quickly breezed through vertebrates (which are all essentially the same for my purposes) and other chordates (for which the data I could find were rather limited). I thought echinoderms would be an easy job, too: there were good in-depth studies of a few species, and they hadn’t revealed anything terribly unusual other than a rearrangement of the Hox cluster in sea urchins (Cameron et al., 2006).

In fact, through comparison with their sister group, the hemichordates (Freeman et al., 2012), it seemed likely that the ancestral echinoderm had a nice, ordered Hox cluster with few if any oddities (Baughman et al., 2014). So I clicked my way to the wonderful Echinobase, which has searchable draft genomes from four of the five living classes of echinoderms (crinoids, a.k.a sea lilies and feather stars, are missing, although a genome in a very early, fragmentary stage exists here). I expected to double-check the published data, collect the same genes from the groups for which Hox papers hadn’t been published, and be off to protostomes in a day or two. Two years later, I still haven’t made it to protostomes, but I’ve gone rather deeper than expected in echinoderms…

(Below: my cast. The main characters are Strongylocentrotus purpuratus [photo: Kirt L. Onthank] and Lytechinus variegatus [photo: Hans Hillewaert] representing sea urchins, Patiria miniata [photo: Jerry Kirkhart] and Acanthaster planci [photo: JSLUCAS75] for sea stars, Parastichopus parvimensis [from here] and Apostichopus japonicus [photo: OpenCage] for sea cucumbers, Metacrinus rotundus [photo: OpenCage] and Anneissia japonica [photo: OpenCage] for crinoids, Ophiothrix spiculata [photo: Jerry Kirkhart] for brittle stars, with supporting acts from Peronella japonica [sea urchins, photo: Endo et al., 2018], Ophiopsila aranea [brittle stars, photo: Bernard Picton], Balanoglossus simodensis [photo: Misaki Marine Biological Station, U of Tokyo], Saccoglossus kowalevskii [photo: Lowe lab] and Ptychodera flava [photo: Moorea BioCode via CalPhotos] for hemichordates, and Branchiostoma floridae [photo via JGI genome portal], Latimeria menadoensis [photo: Claudio Martino] and Callorhinchus milii [photo: fir0002/Flagstaffotos] for chordates. I sourced the photos through Wikipedia/Wikimedia Commons where I could; other sources are linked where applicable.)

cast

You see, I didn’t want to stop at just homeodomains. Homeodomains are cool and important and all, but one thing I’d learned from my earlier forays into the world of Hox genes was that valuable information hid in small patches of conserved sequence elsewhere in their proteins. Besides, I am a pathological perfectionist. I felt a terrible need to collect complete Hox sequences wherever possible.

I already mentioned that sequence similarity between Hoxes outside the homeodomain can be weak to non-existent. I ran into this problem with Echinobase’s brittle star, Ophiothrix spiculata. Using the known sea urchin Hoxes to search its genome, I’d found believable matches for many of them, but the 11/13s defeated me. I had two homeodomains that I thought represented 11/13b and c, but I couldn’t for the life of me recover the rest of the proteins.

The problem with genome databases (or their great advantage depending on your perspective) is that they contain all of the DNA that could be sequenced from the owner of the genome. The problem with Hox genes – most of our genes, in fact – is that they aren’t continuous stretches of DNA. Your typical gene exists in multiple segments (exons) separated by a whole lot of DNA that leaves no trace in the protein product of the gene. (Hox genes normally have two or three exons, the first of which is devoid of homeodomain parts.)

When a gene is expressed, the cell first makes an RNA copy of all that, which is edited to throw out the introns and splice the exons together. That intron-less RNA copy is then carried off to be translated into a protein. Transcriptomes are derived from the RNA copies of active genes. Introns lie forgotten on the cutting room floor: in the sequenced transcripts, one exon continues straight into the next. Therefore, if I could find a brittle star transcriptome, and the 11/13b-c homeodomains in it, perhaps there would be enough of the rest in there to reconstruct those elusive first exons.

Luckily, Delroisse et al. (2016) had published exactly what I needed. In one of their transcriptomes, I found a homeodomain that looked like my Ophiothrix Hox11/13c, as part of a near-complete sequence. Excited, I did the reciprocal search against the Ophiothrix genome…

… and hit neither 11/13b nor 11/13c.

So here I am, staring at a beautiful match between this transcript and a part of the Ophiothrix genome that I hadn’t examined before. The match contains sequence from the first exon, which, given my previous experience with these buggers, is a sure sign that they’re the same gene. And it’s neither of the ones I’d expected.

A bit later in a different database, I hit upon an automatically predicted sea urchin protein that definitely isn’t 11/13b or c either. This is the model sea urchin, S. purpuratus, the one I thought we knew inside out when it came to Hoxes. I check the genome on Echinobase, and lo and behold, there’s the third 11/13b-c type gene, and it’s nowhere near the Hox cluster.

If memory serves, it’s roughly at this point that the words, “What. The. Actual. Fuck. Is. Going. On.” occur in my research notes. (Complete with punctuation.)

I checked the other species on Echinobase. Three 11/13b-c genes again, every time. Over on Genbank, I found a complete protein sequence from a sand dollar that Tsuchimoto and Yamaguchi (2014) had previously classified as 11/13c by exclusion. The Japanese duo had a clear b, but this other sequence was behaving oddly in their phylogenetic analyses. Now I had the obvious explanation: it wasn’t 11/13c at all.*

I wrote to Dave and found out that this was also news to him. By all appearances, I had stumbled on something truly new, in a gene family that’s both iconic in our field, and dear to my obsessive little heart.

We decided to try to turn it into a paper.

In search of the alphabet’s end

Once we’d made that decision, and following Dave’s advice, I had a few tasks ahead of me. I had to check how far back in evolution our new gene (which we called Hox11/13d) went. I had to test whether it had truly escaped the Hox cluster in all of our study species. I had to refresh my memory on deuterostome posterior Hox genes in general, both for paper-writing purposes and in case there was a forgotten reference to our “new” gene lurking somewhere in the literature.

There wasn’t, but.

In a figure legend in Thomas-Chollier et al., 2010), there is a brief mention of an unnamed “Hox11/13c-like” sequence in sea urchins. When I saw that, I damn near soiled myself, but the authors couldn’t definitively identify this sequence as a Hox gene, so they left it at that throwaway comment and a few bits of supplementary data. Luckily, they had a gene ID that I could look up on Echinobase.

Gods help me, it turned out to be another new Hox. When the shock of Hox11/13d had barely worn off, I was confronted with a possible Hox11/13e. And this one wasn’t in the Hox cluster either.

Aside from not being part of the Hox cluster, Hox11/13d is a pretty good echinoderm Hox gene. The homeodomain it encodes is reminiscent of Hox11/13b and c, and, although they are hard for automated searches to find, there are similarities outside the homeodomain that place it firmly in the same group as b-c.

Unlike d, Thomas-Chollier’s “11/13c-like” sequence isn’t that 11/13c-like at all, as you might have guessed from the fact that they weren’t even sure it’s a Hox. The region immediately following the homeodomain (sometimes known as the C-peptide) is very similar to the same part of Hox11/13d. These kinds of motifs can sometimes be used to tell different Hox genes apart. Two C-peptides being strongly similar is a clue that we’re dealing with related genes. However, the homeodomain of Hox11/13e, as we indeed dubbed Thomas-Chollier’s sequence, is really, really weird. It isn’t just unlike 11/13c, it’s unlike anything else I’d seen before. It groups with posterior Hoxes when we test it against a variety of homeodomains, but you wouldn’t know that simply from looking at it.

It is, however, an oddball with a history. As strange as that homeodomain is, once I knew what I was looking for, I found examples in all my other echinoderms. This combination of strong conservation of one Hox gene with considerable differences from other Hox genes just screams “study me more!”, especially when you realise that Hox11/13e appears to be limited to echinoderms (unless something like it is hiding in protostomes…). I looked quite carefully in the hemichordates available to me (Simakov et al., 2015), but the only thing I found that wasn’t one of the “canonical” four posteriors is something called “Abdominal B-like”, which is weird in its own way and not obviously connected to either of our two new genes.

Tangled histories and unhelpful clues

I alluded to the question of Hox11/13b-c origins earlier on. Posterior Hox genes in deuterostomes are notoriously difficult to classify (Ferrier et al., 2000; Thomas-Chollier et al., 2010). When you try to use traditional tree-building methods on them, you get a big unresolved mess, as if the twigs on the tree emerged from an impenetrable mist that hides the arrangement of the older branches from view. Ambulacrarians are definitely the better-behaved half of the Deuterostomia in this regard, since we can say with some confidence that Hox9/10, 11/13a and at least a single precursor to 11/13b-c were present in their last common ancestor.

Nonetheless, two new genes, at least one of which is clearly close to 11/13b-c, complicate matters (Abdominal B-like, as they say in scientist-speak, is beyond the scope of this work). Were they lost in hemichordates? Did echinoderms undergo extra gene duplications, and if so, was it from one or two ancestral genes? Where on earth does Hox11/13e fit? I did a lot of exploratory tree-building for this paper, none of which was particularly helpful in answering those questions.

My other hope was to look at the parts of the protein sequence that led me to my new Hoxes in the first place: all the stuff other than the homeodomain. Using a program called MEME, I found a fair few conserved motifs, but they only seemed to add to the confusion. Hox11/13e, for which I only had first exons (and tentative ones at that) from sea urchins and sea stars, yielded nothing of use apart from its striking C-peptide. In the others, the distribution of motifs created a patchwork of similarities that didn’t neatly align with any one possible history. Echinoderm Hox11/13c mostly did its own thing, while b and d each shared a different subset of motifs with one or both of the hemichordate b-c proteins.

I’m almost inclined to think that there was a single, “prototype” Hox11/13b+ sequence in the ambulacrarian ancestor, which contained all of the motifs I found. In that scenario, separate b and c (and d and maybe e) genes would have evolved independently in hemichordates and echinoderms, and each descendant gene would have lost some of the original motifs more or less at random. Duplicated genes can split the functions of their single ancestor between them (Force et al., 1999), so why not motifs? Short sequence motifs like the ones I was looking for can have important functions, after all. It’s a possibility, but we may never know for sure.

Hox genes gone rogue

I mentioned before that Hox11/13d was outside the Hox cluster. Well, so is Hox11/13e. As far as I can tell, Hox 11/13d and e always reside on separate chunks of the genome form any other Hox gene, including each other. They are always accompanied by neighbouring genes that aren’t Hoxes. Although detachment of a posterior gene from an otherwise apparently intact Hox cluster also happened in ragworms (Hui et al., 2012), it’s still a surprise in echinoderms. Since the relationship between the organisation of Hox genes and their regulation in space and time is… kinda complicated, we can’t really tell what, if anything, all this wandering implies without actually looking at some gene expression.

What are they for?

Then there’s the question of what on earth these genes do. Thanks to Tsuchimoto and Yamaguchi (2014), we know that Hox11/13d is active in later embryonic stages of some sea urchins. It even looks like it might be working with Hox11/13b in a Hox-like fashion, the two of them having adjacent expression domains. We have some transcriptomic evidence that this gene is also active in other sea urchins, brittle stars and starfish, but no idea what it’s doing in any of the above.

We know even less about Hox11/13e. The only evidence for expression I’m aware of is from starfish testicles, and testicles will express any old piece of DNA with an “on” switch. If it’s somehow involved in development, it must be either at very low levels that are difficult to capture in a transcriptome, or at developmental stages that weren’t included in the data I encountered.

If it does have a role in adult echinoderm development, that would be crazy exciting, as both adult echinoderm anatomy and Hox11/13e are so weird and unique. Although they develop from bilaterally symmetrical larvae, adult echinoderms have dispensed with the symmetry that gave Bilateria its name. Instead, like a sea anemone (or a regular anemone…), they are radially symmetrical. Hox genes are involved in both larval and adult development in echinoderms, but from what little I’ve been able to glean from the existing literature, it’s different subsets in larvae and adults rather than the entire Hox cluster together. Is Hox11/13e in the “adult” subset, missed until now due to its unusual sequence? I really hope someone with a lab and a ready supply of baby echinoderms investigates in the near future…

A lesson about expectations

I could go on for a lot longer about this project, but it’s probably time to form some sort of conclusion. For me, perhaps the most important take-home message of this adventure is not what I found, but how and where and why I found it.

I didn’t set out to discover anything. All I wanted to do was collect and organise information already out there. (If a genie popped out of my desk lamp, I might just wish for a full-time job where I get to build my Hox directory… given the volume of genome data already out there and coming out every time I look, continuing this as a hobby project in my free time seems hopelessly Sisyphean now.)

The discovery of Hox11/13d and all that followed was an accidental side effect of my penchant for perfectionism. If I’d contented myself with the homeodomains most students of Hox evolution focus on, I would never have seen a Hox that wasn’t in the books, a Hox I hadn’t expected to exist.

Expectations are important. I’d told myself that I wanted to make sure I had everything, but when my searches spat out a hundred different results, I started to slack off soon after I ticked off the Hoxes I knew. I gave the rest of the hit list a half-hearted effort at best. Hox11/13d has a homeodomain that’s split across two exons, and Hox11/13e is weird. In a search that scores both the closeness and the length of a match, that pushes them to the bottom of the results, where a casual observer, or an observer who thinks they know what they’re looking for, will most likely miss them. I thought I knew that sea urchins had a single, intact(ish) Hox cluster with 11 genes. I’d read a pretty good paper on it. Only the paper wasn’t quite right, after all.

To me, this study stands as a reminder to keep looking. In an era when new genomes are popping up left and right and Big Data with automated analyses is the scientific zeitgeist, it’s still worth rolling your sleeves up, picking up the old magnifying glass and taking a closer look – even in organisms you think you know. You might just chance upon some real treasure.

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Note:

*A “Hox11/13c” behaving oddly should be immediately suspicious based on what I saw in my own trees, where echinoderm Hox11/13c consistently formed a strongly supported group. But that’s hindsight for you…

***

References:

Baughman KW et al. (2014) Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci. Genesis 52:952-958

Cameron RA et al. (2006) Unusual gene order and organization of the sea urchin hox cluster. JEZ B 306:45-58

Delroisse J et al. (2016) De novo adult transcriptomes of two European brittle stars: spotlight on opsin-based photoreception. PLoS ONE 11: e0152988

Duboule D (2007) The rise and fall of Hox gene clusters. Development 134:2549-2560

Endo M et al. (2018) Hidden genetic history of the Japanese sand dollar Peronella (Echinoidea: Laganidae) revealed by nuclear intron sequences. Gene 659:37-43

Ferrier DEK et al. (2000) The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evol Dev 2:284-293

Force A et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545

Freeman R et al. (2012) Identical genomic organization of two hemichordate Hox clusters. Curr Biol 22:2053-2058

Hui JH et al. (2012) Extensive chordate and annelid macrosyntheny reveals ancestral homeobox gene organization. Mol Biol Evol 29:157-165

Simakov O et al. (2015) Hemichordate genomes and deuterostome origins. Nature 527:459-465

Szabó R and Ferrier DEKF (2018) Two more Posterior Hox genes and Hox cluster dispersal in echinoderms. BMC Evol Biol 18:203

Thomas-Chollier M et al. (2010) A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution. BMC Evol Biol 10:73

Tsuchimoto J and Yamaguchi M (2014) Hox expression in the direct-type developing sea urchin Peronella japonica. Dev Dyn 243:1020-1029

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To dump a chunk of trunk

The Mammal has deemed that Hox genes and good old-fashioned feel-good evo-devo are a good way to blink back to life*. Also, tardigrades. Tardigrades are awesome. Here is one viewed from above, from the Goldstein lab via Encyclopedia of Life:

hypsibius_dujardini_eol

Tardigrades or water bears are also a bit unusual. Their closest living relatives are velvet worms (Onychophora) and arthropods. Exactly who’s closest to whom in that trio of phyla collectively known as the Panarthropoda is not clear, and I don’t have the energy to wade into the debate – besides, it’s not really important for the purposes of this post. What Smith et al. (2016) concluded about these adorably indestructible little creatures holds irrespective of their precise phylogenetic position.

Anyway. I said tardigrades were unusual, and I don’t mean their uncanny ability to survive the apocalypse and pick up random genes in the process (Boothby et al., 2015). (ETA: so apparently there may not be nearly as much foreign gene hoarding as the genome paper suggests – see Sujai Kumar’s comment below! Doesn’t change the fact that tardigrades are tough little buggers, though 🙂 ) The oddity we’re interested in today lies in the fact that all known species are built to the exact same compact body plan. Onychophorans and many arthropods are elongated animals with lots of segments, lots of legs, and often lots of variation in the number and type of such body parts. Tardigrades? A wee head, four chubby pairs of legs, and that’s it.

How does a tardigrade body relate to that of a velvet worm, or a centipede, or a spider? Based solely on anatomy, that’s a hell of a question to answer; even the homology of body parts between different kinds of arthropods can be difficult to determine. I have so far remained stubbornly uneducated on the minutiae of (pan)arthropod segment homologies, although I do see papers purporting to match brain parts, appendages and suchlike between different kinds of creepy-crawlies on a fairly regular basis. Shame on me for not being able to care about the details, I guess – but the frequency with which the subject comes up suggests that the debate is far from over.

Now, when I was first drawn to the evo-devo field, one of the biggest attractions was the notion that the expression of genes as a body part forms can tell us what that body part really is even when anatomical clues are less than clear. That, of course, is too good to be simply true, but sometimes the lure of genes and neat homology stories is just too hard to resist. Smith et al.‘s investigation of tardigrade Hox genes is definitely that kind of story.

Hox genes are generally a good place to look if you’re trying to decipher body regions, since their more or less neat, orderly expression patterns are remarkably conserved between very distantly related animals (they are probably as old as the Bilateria, to be precise). A polychaete worm, a vertebrate and an arthropod show the same general pattern – there is no active Hox gene at the very front of the embryo, then Hoxes 1, 2, 3 and so on appear in roughly that order, all the way to the rear end. There are variations in the pattern – e.g. the expression of a gene can have sharp boundaries or fade in and out gradually; different genes can overlap to different extents, the order isn’t always perfect, etc. – but staggered Hox gene expression domains, with the same genes starting up in the same general area along the main body axis, can be found all across the Bilateria.

Tardigrades are no exception, in a sense – but they are also quite exceptional. First, their complement of Hox genes is a bit of a mess. At long last, we have a tardigrade genome to hand, in which Smith et al. (2016) found good honest Hox genes. What they didn’t find was a Hox cluster, an orderly series of Hox genes sitting like beads on a DNA string. Instead, the Hox genes in Hypsibius dujardini, the sequenced species, are all over the genome, associating with all kinds of dubious fellows who aren’t Hoxes.

What Smith et al. also didn’t find was half of the Hox genes they expected. A typical arthropod has ten or so Hox genes, a pretty standard ballpark for an animal that isn’t a vertebrate. H. dujardini has only seven, three of which are triplicates of Abdominal-B, a gene that normally exists in a single copy in arthropods. So basically, only five kinds of Hox gene – number two and most of the “middle” ones are missing. What’s more, two more tardigrades that aren’t closely related to H. dujardini also appear to have the same five Hox gene types (though only one Abd-B each), so this massive loss is probably a common feature of Tardigrada. (No word on whether the scattering of the Hox  cluster is also shared by the other two species.)

We know that the genes are scattered and decimated, but are their expression patterns similarly disrupted? You don’t actually need an intact Hox cluster for orderly Hox expression, and indeed, tardigrade Hox genes are activated in a perfectly neat and perfectly usual pattern that resembles what you see in their panarthropod cousins. Except for the bit where half the pattern is missing!

Here’s part of Figure 4 from the paper, a schematic comparison of tardigrade Hox expression to that of other panarthropods – a generic arachnid, a millipede and a velvet worm. (otd is a “head” gene that lives in the Hox-free anterior region; lab is the arthropod equivalent of Hox1, Dfd is Hox4, and I’m not sure which of Hox6-8 ftz is currently supposed to be.) The interesting thing about this is that according to Hox genes, the entire body of the tardigrade corresponds to just the front end of arthropods and velvet worms.

Smith_etal2016-hox_tardigrade_fig4A

In addition, one thing that is not shown on this diagram is that Abdominal-B, which normally marks the butt end of the animal, is still active in the tardigrade, predictably in the last segment (L4, that is). So if you take the Hox data at face value, a tardigrade is the arse end of an arthropod tacked straight onto its head. Weird. It’s like evolution took a perfectly ordinary velvet worm-like creature and chopped out most of its trunk.

The tardigrade data suggest that the original panarthropod was probably more like arthropods and velvet worms than tardigrades – an elongated animal with many segments. The strange tardigrade situation can’t be the ancestral one, since the Hox genes that tardigrades lack long predate the panarthropod ancestor. Now, it might be possible to lose half your Hox genes while keeping your ancestral body plan, but an unusual body plan and an unusual set of Hox genes is a bit of a big coincidence, innit?

Smith et al. point out that the loss of the Hox genes was unlikely to be the cause of the loss of the trunk region – Hox genes only specify what grows on a segment, they don’t have much say in how many segments develop in the first place. Instead, the authors reason, the loss of the trunk in the tardigrade ancestor probably made the relevant Hox genes dispensable.

Damn, this story makes me want to see the Hox genes of all those oddball lobopodians from the Cambrian. Some of them are bound to be tardigrade relatives, right?

***

References:

Boothby TC et al. (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PNAS 112:15976-15981

Smith FW et al. (2016) The compact body plan of tardigrades evolved by the loss of a large body region. Current Biology 26:224-229

***

*The Mammal has been pretty depressed lately. As in mired up to her head in weird energy-sucking flu. Unfortunately, writing is one of those things that the damn brain monster has eaten most of the fun out of. Also, I have a shitty normal person job at the moment, and shitty job taking up time + barely enough motivation to crawl out of bed and pretend to be human means I have, at best, one afternoon per week that I actually spend on catching up with science. That is just enough to scroll through my feeds and file away the interesting stuff, but woefully insufficient for the writing of posts, not to mention that my ability to concentrate is, to be terribly technical, absolutely fucked. It’s not an ideal state of affairs by any stretch, and I’m pretty sure that if I made more of an effort to read and write about cool things, it would pay off in the mental health department, but… well. That sort of reasonable advice is hard to hear with the oozing fog-grey suckers of that thing clamped onto my brain.

The things you can tell from a pile of corpses…

I’m really late to this party, but I never claimed to be timely, and the thing about the reproductive habits of Fractofusus is too interesting not to cover.* Rangeomorphs  like Fractofusus are really odd creatures. They lived in that Ediacaran twilight zone between older Precambrian seas devoid of macroscopic animals and younger Cambrian seas teeming with recognisable members of modern groups. Rangeomorphs such as RangeaCharnia and Fractofusus itself have such a unique fractal body plan (Narbonne, 2004) that no one really knows what they are. Although they were probably not photosynthetic like plants or algae (they are abundant in deep sea sediments where there wouldn’t have been enough light), their odd body architectures are equally difficult to compare to any animal that we know.

Mitchell et al. (2015) don’t bring us any closer to the solution of that mystery; they do, however, use the ultimate power of Maths to deduce how the enigmatic creatures might have reproduced. Fractofusus is an oval-shaped thingy that could be anywhere from 1 cm to over 40 cm in length. Unlike some other rangeomorphs, it lay flat on the seafloor with no holdfasts or stalks to be seen. Fractofusus fossils are very common in the Ediacaran deposits of Newfoundland. Since there are so many of them, and there is no evidence that they were capable of movement in life, the researchers figured their spatial distribution might offer some clues as to their reproductive habits. A bit of seafloor covered in Fractofusus might look something like this (drawing from the paper):

clusters within clusters

(The lines between individuals don’t actually come from the fossils, they just represent the putative connection between a parent and its babies.)

Statistical models suggest that the fossils are not randomly distributed but clearly clustered: small specimens around medium-sized ones, which are in turn gathered around the big guys. Two out of three populations examined show these clusters-within-clusters; the third has only one layer of clustering, but it’s still far from random. As the authors note, the real populations they studied involve a lot more specimens than shown in the diagram, but they “rarefied” them a bit for clarity of illustration while keeping their general arrangement.

The study looked not only at the distances between small, medium and large specimens, but also directions – both of where the specimens were and which way they pointed. If young Fractofusus spread by floating on the waves, they’d be influenced by currents in the area. It seems the largest specimens were – they are unevenly distributed in different directions. In contrast, smaller individuals were clustered around the bigger ones without regard to direction. Small and large specimens alike pointed randomly every which way.

What does this tell us about reproduction? The authors conclude that the big specimens probably arrived on the current as waterborne youngsters, hence their arrangement along particular lines . However, once there, they must have colonised their new home in a way that doesn’t involve currents. Mitchell et al. think that way was probably stolons – tendrils that grew out from the parent and sprouted a new individual at the end. This idea is further strengthened by the fact that among thousands of specimens, not a single one shows evidence for other types of clonal reproduction – no fragments, and no budding individuals, are known. (Plus if a completely sessile organism fragments, surely the only way the pieces could spread anywhere would be by riding currents, and that would show up in their distribution.)

Naturally, none of this tells us whether Fractofusus was an animal, a fungus or something else entirely. Sending out runners is not a privilege of a particular group, and while there is evidence that the original founders of the studied populations came from far away on the waves, we have no idea what it was that floated in to take root in those pieces of ancient seafloor. Was it a larva? A spore? A small piece of adult tissue? Damned if we know. Despite what Wikipedia and news headlines would have you believe, there is nothing to suggest that sex was involved. It may have been, but the evidence is silent on that count. (Annoyingly, the news articles themselves acknowledge that. Fuck headlines is all I’m saying…)

While sometimes we gain insights into ancient reproductive habits via spectacular fossils like brooding dinosaurs or pregnant ichthyosaurs, this study is a nice reminder that in some cases, a lot can be deduced even in the absence of such blatant evidence. This was an interesting little piece of Precambrian ecology, and a few remarks in the paper suggest more to come: “Other taxa exhibit an intriguing range of non-random habits,” the penultimate paragraph says, “and our preliminary analyses indicate that Primocandelabrum and Charniodiscus may have also reproduced using stolons.”

An intriguing range of non-random habits? No citations? I wanna know what’s brewing!

***

*Also, I’ve got to write something so I can pat myself on the back for actually achieving something beyond getting out of bed. Let’s just say Real Life sucks, depression sucks worse, and leave it at that.

***

References:

Mitchell EG et al. (2015) Reconstructing the reproductive mode of an Ediacaran macro-organism. Nature 524:343-346

Narbonne GM (2004) Modular construction of Early Ediacaran complex life forms. Science 305:1141-1144

Putting the cart before the… snake?

Time to reexamine some assumptions (again)! And also, talk about Hox genes, because do I even need a reason?

Hox genes often come up when we look for explanations for various innovations in animal body plans – the digits of land vertebrates, the limbless abdomens of insects, the various feeding and walking and swimming appendages of crustaceans, the strongly differentiated vertebral columns of mammals, and so on.

Speaking of differentiated vertebral columns, here’s one group I’d always thought of as having pretty much the exact opposite of them: snakes. Vertebral columns are patterned, among other things, by Hox genes. Boundaries between different types of vertebrae such as cervical (neck) and thoracic (the ones bearing the ribcage) correspond to boundaries of Hox gene expression in the embryo – e.g. the thoracic region in mammals begins where HoxC6 starts being expressed.

In mammals like us, and also in archosaurs (dinosaurs/birds, crocodiles and extinct relatives thereof), these boundaries can be really obvious and sharply defined – here’s Wikipedia’s crocodile skeleton for an example:

In contrast, the spine of a snake (example from Wikipedia below) just looks like a very long ribcage with a wee tail:

Snakes, of course, are rather weird vertebrates, and weird things make us sciencey types dig for an explanation.

Since Hox genes appear to be responsible for the regionalisation of vertebral columns in mammals and archosaurs, it stands to reason that they’d also have something to do with the comparative lack of regionalisation (and the disappearance of limbs) seen in snakes and similar creatures. In a now classic paper, Cohn and Tickle (1999) observed that unlike in chicks, the Hox genes that normally define the neck and thoracic regions are kind of mashed together in embryonic pythons. Below is a simple schematic from the paper showing where three Hox genes are expressed along the body axis in these two animals. (Green is HoxB5, blue is C8, red is C6.)

Cohn_Tickle1999_hoxRegions

As more studies examined snake embryos, others came up with different ideas about the patterning of serpentine spines. Woltering et al. (2009) had a more in-depth look at Hox gene expression in both snakes and caecilians (limbless amphibians) and saw that there are in fact regions ruled by different Hoxes in these animals, if a little fuzzier than you’d expect in a mammal or bird – but they don’t appear to translate to different anatomical regions. Here’s their summary of their findings, showing the anteriormost limit of the activity of various Hox genes in a corn snake compared to a mouse:

Woltering_etal2009-mouse_vs_snake

Such differences aside, both of the above studies operated on the assumption that the vertebral column of snakes is “deregionalised” – i.e. that it evolved by losing well-defined anatomical regions present in its ancestors. But is that actually correct? Did snakes evolve from more regionalised ancestors, and did they then lose this regionalisation?

Head and Polly (2015) argue that the assumption of deregionalisation is a bit stinky. First, that super-long ribcage of snakes does in fact divide into several regions, and these regions respect the usual boundaries of Hox expression. Second, ordinary lizard-shaped lizards (from which snakes descended back in the days of the dinosaurs) are no more regionalised than snakes.

The study is mostly a statistical analysis of the shapes of vertebrae. Using an approach called geometric morphometrics, it turned these shapes from dozens of squamate (snake and lizard) species into sets of coordinates, which could then be compared to see how much they vary along the spine and whether the variation is smooth and continuous or clustered into different regions. The authors evaluated hypotheses regarding the number of distinct regions to see which one(s) best explained the observed variation. They also compared the squamates to alligators (representing archosaurs).

The results were partly what you’d expect. First, alligators showed much more overall variation in vertebral shape than squamates. Note that that’s all squamates – leggy lizards are nearly (though not quite) as uniform as their snake-like relatives. However, in all squamates, the best-fitting model of regionalisation was still one with either three or four distinct regions in front of the hips/cloaca, and in the majority, it was four, the same number as the alligator had.

Moreover, there appeared to be no strong support for an evolutionary pattern to the number of regions – specifically, none of the scenarios in which the origin of snake-like body plans involved the loss of one or more regions were particularly favoured by the data. There was also no systematic variation in the relative lengths of various regions; the idea that snakes in general have ridiculously long thoraxes is not supported by this analysis.

In summary, snakes might show a little less variation in vertebral shape than their closest relatives, but they certainly didn’t descend from alligator-style sharply regionalised ancestors, and they do still have regionalised spines.

Hox gene expression is not known for most of the creatures for which vertebral shapes were analysed, but such data do exist for mammals (mice, here), alligators, and corn snakes. What is known about different domains of Hox gene activation in these three animals turns out to match the anatomical boundaries defined by the models pretty well. In the mouse and alligator, Hox expression boundaries are sharp, and the borders of regions fall within one vertebra of them.

In the snake, the genetic and morphological boundaries are both gradual, but the boundaries estimated by the best model are always within the fuzzy boundary region of an appropriate Hox gene expression domain. Overall, the relationship between Hox genes and regions of the spine is pretty consistent in all three species.

To finish off, the authors make the important point that once you start turning to the fossil record and examining extinct relatives of mammals, or archosaurs, or squamates, or beasties close to the common ancestor of all three groups (collectively known as amniotes), you tend to find something less obviously regionalised than living mammals or archosaurs – check out this little figure from Head and Polly (2015) to see what they’re talking about:

Head_Polly2015-phylogeny_of_spines

(Moving across the tree, Seymouria is an early relative of amniotes but not quite an amniote; Captorhinus is similarly related to archosaurs and squamates, Uromastyx is the spiny-tailed lizard, Lichanura is a boa, Thrinaxodon is a close relative of mammals from the Triassic, and Mus, of course, is everyone’s favourite rodent. Note how alligators and mice really stand out with their ribless lower backs and suchlike.)

Although they don’t show stats for extinct creatures, Head and Polly argue that mammals and archosaurs, not snakes, are the weird ones when it comes to vertebral regionalisation. For most of amniote evolution, the norm was the more subtle version seen in living squamates. It was only during the origin of mammals and archosaurs that boundaries were sharpened and differences between regions magnified. Nice bit of convergent/parallel evolution there!

***

References:

Cohn MJ & Tickle C (1999) Developmental basis of limblessness and axial patterning in snakes. Nature 399:474-479

Head JJ & Polly PD (2015) Evolution of the snake body form reveals homoplasy in amniote Hox gene function. Nature 520:86-89

Woltering JM et al. (2009) Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code. Developmental Biology 332:82-89

Finally, that sponge ParaHox gene

ParaHox genes are a bit like the underappreciated sidekicks of Hox genes. Or little sisters, as the case may be, since the two families are closely related. Hox genes are probably as famous as anything in evo-devo. Being among the first genes controlling embryonic development to be (a) discovered, (b) found to be conserved between very distantly related animals, they are symbolic of the late 20th century evo-devo revolution.

ParaHoxes get much less attention despite sharing some of the most exciting properties of Hox genes. Like those, they are involved in anteroposterior patterning – that is, partitioning an embryo along its head to tail axis. Also like Hox genes, they are often neatly clustered in the genome, and when they are, they tend to be expressed in the same order (both in space and time) in which they sit in the cluster*. Their main ancestral roles for bilaterian animals seem to be in patterning the gut and the central nervous system (Garstang and Ferrier, 2013).

There are three known types of ParaHox gene, which are generally thought to be homologous to specific Hox subsets of Hox genes – by the most accepted scheme, Gsx is the closest sister of Hox1 and Hox2, Xlox is closest to Hox3, and Cdx to Hox9 and above. It is abundantly clear that Hoxes and ParaHoxes are closely related, but there has been a bit of debate concerning the number of genes in the ancestral gene cluster that gave rise to both – usually called “ProtoHox” (Garcia-Fernàndez, 2005).

Another big question about these genes is precisely when they originated, and in this regard, ParaHox genes are proving much more interesting than Hoxes. You see, there are plenty of animals with both Hox and ParaHox genes, which is what you’d expect given the ProtoHox hypothesis, but there are also animals with only ParaHoxes. If there really was a ProtoHox gene/cluster that then duplicated to give rise to Hoxes and ParaHoxes, then lone ParaHoxes (or Hoxes for that matter) shouldn’t happen – unless the other cluster was lost along the way.

So a suspiciously Gsx-like gene in the weird little blob-creature Trichoplax, which has nothing remotely resembling a Hox gene, was a big clue that (a) Hox/ParaHox genes might go back further in animal evolution than we thought, (b) the loss of the entire Hox or ParaHox cluster is totally possible**, despite how fundamental these genes appear to be for correctly building an animal.

I wrote (at length) about a study by Mendivil Ramos et al. (2012), which revealed that while Trichoplax had no Hox genes and only one of the three types of ParaHox gene, it preserved the more or less intact genomic neighbourhoods in which Hox and ParaHox clusters are normally situated. One of the more interesting results of that paper was that the one sponge genome available at the time – that of Amphimedon queenslandica, which had no trace of either Hox or ParaHox genes – also contained statistically significant groupings of Hox and ParaHox neighbour genes, as if it had a Hox neighbourhood and a ParaHox neighbourhood, but the Hoxes and ParaHoxes themselves had moved out.

That study thus pointed towards an intriguing hypothesis, previously championed by Peterson and Sperling (2007) based solely on gene phylogenies: sponges once did have Hox and ParaHox genes/clusters, which at least some of them later lost. This would essentially mean that the two gene clusters go straight back to the origin of animals if not further***, and we may never find any surviving remnant of the ancestral ProtoHox cluster, since the closest living relatives of animals have neither the genes nor their neighbourhoods (that we know of).

Hypotheses are nice, but as we know, they do have a tendency to be tragically slain by ugly facts. Can we further test this particular hypothesis about sponges? Are there facts that could say yay or nay? (Of course there are. I wouldn’t be writing this otherwise 😉 )

I keep saying that we should always be careful when generalising from one or a few model organisms, that we ignore diversity in the animal kingdom at our own peril, and that “distantly related to us” = “looks like our distant ancestors” is an extremely dodgy assumption. Well, here’s another lesson in that general vein: unlike Amphimedon, some sponges have not just the ghosts of vanished ParaHox clusters, but intact, honest to god ParaHox genes!

It’s calcareous sponges again. Sycon ciliatum and Leucosolenia complicata, two charming little calcisponges, recently had their genomes sequenced (alas, they weren’t yet public last time I checked), and since then, there’s been a steady stream of “cool stuff we found in calcisponge genomes” papers from Maja Adamska’s lab and their collaborators. I’ve discussed one of them (Robinson et al., 2013), in which the sponges revealed their rather unhelpful microRNAs, and back in October (when I was slowly self-destructing from thesis stress), another study announced a couple of delicious ParaHoxes (Fortunato et al., 2014).

(Exciting as it is, the paper starts by tickling my pet peeves right off the bat by calling sponges “strong candidates for being the earliest extant lineage(s) of animals”… I suppose nothing can be perfect… *sigh*)

The study actually covers more than just (Para)Hox genes; it looks at an entire gene class called Antennapedia (ANTP), which includes Hoxes and ParaHoxes plus a handful of related families I’m far less interested in. Sycon and Leucosolenia don’t have a lot of ANTP genes – only ten in the former and twelve in the latter, whereas a typical bilaterian like a fruit fly or a lancelet has several times that number – but from phylogenetic analyses, these appear to be a slightly different assortment of genes from those present in Amphimedon, the owner of the first sequenced sponge genome. This picture is most consistent with a scenario in which all of the ANTP genes in question were present in our common ancestor with sponges, and each sponge lineage lost some of them independently. (You may not realise this until you start delving into the history of various gene families, but genes come and go a LOT in evolution.)

Sadly, many of the branches on these gene trees are quite wonky, including the one linking a gene from each calcisponge to the ParaHox gene Cdx. However, somewhat fuzzy trees are not the only evidence the study presents. First, the putative sponge Cdxes possess a little motif in their protein sequences that is only present in a handful of gene families within the ANTP class. If you take only these families rather than everything ANTP and make trees with them, the two genes come out as Cdx in every single tree, and with more statistical support than the global ANTP trees gave them. Another motif they share with all Hoxes, ParaHoxes and a few of their closest relatives, but not with other ANTP class families.

Second, at least the gene in Sycon appears to have the right neighbours (Leucosolenia was not analysed for this). Since the Sycon genome sequence is currently in pieces much smaller than whole chromosomes, only four or so of the genes flanking ParaHox clusters in other animals are clearly linked to the putative Cdx in the sponge. However, when the researchers did the same sort of simulation Mendivil Ramos et al. (2012) did for Amphimedon, testing whether Hox neighbours and ParaHox neighbours found across all fragments of the genome are (a) close to other Hox/ParaHox neighbours or randomly scattered (b) mixed or segregated, they once again found cliques of genes with little overlap, indicating the once-existence of separate Hox and ParaHox clusters.

Fortunato et al. (2014) also examined the expression of their newfound Cdx gene, and found it no less intriguing than its sequence or location in the genome, although their description in the paper is very limited (no doubt because they’re trying to cram results on ten genes into a four-page Nature paper). The really interesting activity they mention and picture is in the inner cell mass of the young sponge in its post-larval stages – the bit that develops into the lining of its feeding chambers. Which, Adamska’s team contend, may well be homologous to our gut lining. In bilaterians, developing guts are one of the major domains of Cdx and ParaHox genes in general!

So at least three different lines of evidence – sequence, neighbours and expression – make this picture hang together quite prettily. It’s incredibly cool – the turning on their heads of long-held assumptions is definitely the most exciting part of science, I say! On the other hand, it’s also a little disheartening, because now that everyone in the animal kingdom except ctenophores has definitive ParaHox genes and at least the empty seats once occupied by Hox genes, are we ever going to find a ProtoHox thingy? May it be that it’ll turn up in one of the single-celled beasties people like Iñaki Ruiz-Trillo are sequencing? That would be cool and weird.

The coolest twist on this story, though, would be to discover traces of ProtoHoxes in a ctenophore, since solid evidence for ProtoHox-wielding ctenophores would (a) confirm the strange and frankly quite dubious-sounding idea that ctenophores, not sponges, are the animal lineage farthest removed from ourselves, (b) SHOW US A FREAKING PROTOHOX CLUSTER. (*bounces* >_> Umm, * cough* OK, maturity can suck it 😀 ) However, given how horribly scrambled at least one ctenophore genome is (Ryan et al., 2013), that’s probably a bit too much to ask…

***

Notes

*Weirdly, the order of expression in time is the opposite of that of the Hox cluster. In both clusters, the “anterior” gene(s), i.e. Hox1-2 or Gsx, are active nearest the front of the embryo, but while anterior Hox genes are also the earliest to turn on, in the ParaHox cluster the posterior gene (Cdx) wakes up first. /end random trivia

**Of course we’ve long known that losing a Hox cluster is not that big a deal, but previously, all confirmed losses occurred in animals with more than one Hox cluster to begin with – a fish has plenty of Hox genes left even after chucking an entire set of them.

***With the obligatory ctenophore caveat

***

References

Fortunato SAV et al. (2014) Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature 514:620-623

Garcia-Fernàndez J (2005) The genesis and evolution of homeobox gene clusters. Nature Reviews Genetics 6:881-892

Garstang M & Ferrier DEK (2013) Time is of the essence for ParaHox homeobox gene clustering. BMC Biology 11:72

Mendivil Ramos O et al. (2012) Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals. Current Biology 22:1951-1956

Peterson KJ & Sperling EA (2007) Poriferan ANTP genes: primitively simple or secondarily reduced? Evolution and Development 9:405-408

Robinson JM et al. (2013) The identification of microRNAs in calcisponges: independent evolution of microRNAs in basal metazoans. Journal of Experimental Zoology B 320:84-93

Ryan JF et al. (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342:1242592

A bit of Hox gene nostalgia

I had the most random epiphany over my morning tea today. I don’t even know what got me thinking about the Cambrian explosion (as if I needed a reason…). Might have been remembering something from the Euro Evo Devo conference I recently went to. (I kind of wanted to post about that, because I saw some awesome things, but too much effort. My brain isn’t very cooperative these days.)

Anyway.

I was thinking about explanations of the Cambrian explosion and remembering how the relevant chapter in The Book of Life (otherwise known as the book that made me an evolutionary biologist)  tried to make it all about Hox genes. It’s an incredibly simplistic idea, and almost certainly wrong given what we now know about the history of Hox genes (and animals)*. At the time, and for a long time afterwards, I really wanted it to be true because it appeals to my particular biases. But I digress.

Then it dawned on me just how new and shiny Hox genes were when this book was written. I thought, holy shit, TBoL is old. And how far evo-devo as a field has come since!

The Book of Life was first published in 1993. That is less than a decade after the discovery of the homeobox in fruit fly genes that controlled the identity of segments (McGinnis et al., 1984; Scott and Weiner, 1984), and the finding that homeoboxes were shared by very distantly related animals (Carrasco et al., 1984). It was only four years after the recognition that fly and vertebrate Hox genes are activated in the same order along the body axis (Graham et al., 1989; Duboule and Dollé, 1989).

This was a HUGE discovery. Nowadays, we’re used to the idea that many if not most of the genes and gene networks animals use to direct embryonic development are very ancient, but before the discovery of Hox genes and their clusters and their neatly ordered expression patterns, this was not at all obvious. What were the implications of these amazing, deep connections for the evolution of animal form? It’s not surprising that Hox genes would be co-opted to explain animal evolution’s greatest mysteries.

It also occurred to me that 1993 is the year of the zootype paper (Slack et al., 1993). Slack et al. reads like a first peek into a brave new world with limitless possibilities. They first note the similarity of Hox gene expression throughout much of the animal kingdom, then propose that this expression pattern (their “zootype”) should be the definition of an animal. After that, they speculate that just as the pattern of Hox genes could define animals, the patterns of genes controlled by Hoxes could define subgroups within animals. Imagine, they say, if we could solve all those tough questions in animal phylogeny by looking at gene expression.

As always, things turned out More Complicated, what with broken and lost Hox clusters and all the other weird shit developmental “master” genes get up to… but it was nice to look back at the bright and simple childhood of my field.

(And my bright and simple childhood. I read The Book of Life in 1998 or 1999, not entirely sure, and in between Backstreet Boys fandom, exchanging several bookfuls of letters with my BFF and making heart-shaped eyes at long-haired guitar-playing teenage boys, I somehow found true, eternal, nerdy love. *nostalgic sigh*)

***

*Caveat: it’s been years since I last re-read the book, and my copy is currently about 2500 km from me, so the discussion of the Cambrian explosion might be more nuanced than I remember. Also, my copy is the second edition, so I’m only assuming that the Hox gene thing is there in the original.

***

References:

Carrasco AE et al. (1984) Cloning of an X. laevis gene expressed during early embryogenesis coding for a peptide region homologous to Drosophila homeotic genes. Cell 37:409-414

Duboule D & Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. The EMBO Journal 8:1497-1505

Graham A et al. (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367-378

McGinnis W et al. (1984) A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. Nature 308:428-433

Scott MP & Weiner AJ (1984) Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. PNAS 81:4115-4119

Slack JMW et al. (1993) The zootype and the phylotypic stage. Nature 361:490-492

About X-frogs and failing at regeneration

Not the usual mad squee, but here’s a neat little system for studying regeneration that I quite liked today. I normally think about regeneration in terms of amputated limbs, mutilated hearts, decapitated flatworms. But you can induce a kind of “regeneration” in a less drastic and rather more tricksy way, at least in some animals. In newts and salamanders, you can create a small, superficial wound on the side of a limb, then manipulate a nearby nerve into it and add some skin from the other side of the limb.

The poor hurt limb then decides you’ve actually cut something off and tells the wound to grow a new limb. If you don’t add skin, regeneration begins but doesn’t progress very far; if you don’t add a nerve, nothing happens. IIRC you can also make extra heads in some worms in a similar way, but I digress. The figure below from Endo et al. (2004) illustrates just how well the procedure can work. The top row shows stages in the development of the extra limb, while D shows the stained skeletons of the original and new limbs. I’d say that’s a pretty good looking forearm and hand!

Endo_etal2004-ectopicLimb

 

That this trick works is in itself a very interesting insight into the nature of regeneration, as it helps us figure out exactly what it is that triggers various steps of regeneration as opposed to a simple healing process (Endo et al., 2004).

Clawed frogs (Xenopus) have been staples of embryology for a long time, but they are also quite fascinating from a regeneration point of view. One, they can regrow their limbs while they are tadpoles, but mostly lose the ability as they mature. They also have a really weird thing going on with their tadpole tails, which they can regenerate early on, then can’t, then can again (Slack et al., 2004). Huh? O.o

Two, their adult limb regeneration ability is not totally absent: it’s somewhere between salamanders’ (oh, whatever, fine, I can do that!) and ours (uh… as long as I’m a baby and it’s just a fingertip?). In a frog, an amputated arm or leg doesn’t simply heal over, but the… thing that grows out of the stump is just a simple cartilaginous spike with no joints or muscles. It’s as if the system was trying very hard to remember how to form a limb but kind of got distracted.

We are obviously interested in creating superhumans with mad regeneration skillz, which also makes us interested in how and why animals lose this seemingly very useful ability*. (Bely (2010) wrote a lovely piece on this not at all simple question.) So: Xenopus yay!

Now, Mitogawa et al. (2014) have devised a skin wound + nerve deviation system to grow little extra limb buds in adult frogs. As you might expect, it doesn’t work nearly as well as it does in axolotls: you need three nerves rather than one, and it only induces a bud about half the time, but it works well enough for research purposes.

The bud (technically, a blastema when you’re talking about regeneration) looks like a good regeneration blastema: it’s got the seemingly undifferentiated cells inside, it’s got the thickened epidermis at the tip that teams up with the nerves to give developmental instructions to the rest of the thing, and it expresses a whole bunch of genes that are turned on in normal limb blastemas.

(Totally random aside: thanks to Chrome’s spell checker, I have discovered that “blastema” is an anagram for “lambaste”.)

One area where this blastema-by-trickery fails is making cartilage, which is one of the few proper limb things the defective spike regenerates in frogs do contain. There’s no simple way of coaxing a complete spike out of these blastemas. The researchers tried the skin graft thing from axolotls (which can already form cartilage without the skin graft), but they still only got a little blastema with no cartilage. To get a skeleton, however crappy,  you need to cut out muscles and crack the underlying bone, which kind of defeats the purpose of the whole exercise IMO. At that point, you might as well just chop off the arm.

Below: the best a frog can do. Development of blastema-like bumps and “spike limbs” on the upper arm from Mitogawa et al. (2014). Compared to the fully formed accessory limbs of axolotls, the things you can see in B-D here are not terribly impressive, but they may be just the “transitional form” we need!

The failure of skin grafts alone at inducing cartilage, however, does hint at the things that go wrong with regeneration in frogs. Mitogawa et al. speculate that newt and axolotl limbs produce factors that frogs can only get from damaged bone. Broken bones even in us form a cartilaginous callus as they begin to heal, and unlike the cartilage in the extra limbs of axolotls, the cartilage in frog spikes is directly attached to the underlying bone.

They also point out that if you add proteins called BMPs to amputated mouse arms, which are otherwise even shitter at regeneration than frog arms, a surprising amount of bone formation occurs. (“BMP” stands for bone morphogenetic protein, which is a big clue to their function.) So it looks like there may be a kind of regeneration gradient from mammals (need bone damage AND extra BMP), through frogs (need bone damage, take care of BMPs themselves) to salamanders (don’t need either).

I should point out that salamanders and frogs are equally closely related to us, so this isn’t a proper evolutionary gradient, but given all the ways in which we and amphibians are fundamentally similar, our loss of regenerative ability may well have evolved through a similar stage to where frogs are now. Neat!

(I just wish they stopped calling us “higher vertebrates”. That phrase annoys me right up the fucking wall, because, and I may have said this before, EVOLUTION IS NOT A GODDAMNED LADDER. The group they are referring to has a perfectly good name that doesn’t imply ladder thinking. Amniotes, people. Or mammals, if you mean mammals, but I think if they’d meant mammals they would have said mammals. End grump.)

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*I mean “us” in a very general sense. I think regenerative medicine is the coolest thing in medicine since vaccines and antibiotics, but I personally don’t think that the evolution of regenerative ability needs medical considerations to make it interesting. Whatever. I’m not exactly a practically minded person 😛

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References:

Bely AE (2010) Evolutionary loss of animal regeneration: pattern and process. Integrative and Comparative Biology 50:515-527

Endo T et al. (2004) A stepwise model system for limb regeneration. Development 270:135-145

Mitogawa K et al. (2014) Ectopic blastema induction by nerve deviation and skin wounding: a new regeneration model in Xenopus laevis. Regeneration 2:11

Slack JMW et al. (2004) Cellular and molecular mechanisms of regeneration in Xenopus. Philosophical Transactions of the Royal Society B 359:745-751

Catching up

So I felt like I couldn’t put off the sixteen hundred articles twiddling their thumbs and tapping their feet in my RSS reader any longer. This is the first part of the crop that has accumulated since late December (yikes!). Legless axolotls, homing starfish, secretly related proteins, and more!

1. Axolotls are good at regenerating – until you make them grow up.

(Portrait of a pale lab/aquarium variety axolotl by Orizatriz, Wiki Commons.)

It’s probably not exactly obvious from my posting record, but a large part of my PhD work is about regeneration. It’s something we humans are pretty shit at, but many other vertebrates aren’t. Axolotls, these adorably dumb-faced salamanders, can easily regrow their legs. However, lab axolotls are kind of permanent babies. Although they can grow up in the sense that they are able to breed, they normally keep larval characteristics like gills throughout their lives. It’s reasonable to suspect that this influences their regenerative ability – after all, tadpoles lose their ability to regrow limbs the moment they turn into frogs.

It’s possible to make axolotls metamorphose, too, if you treat them with thyroxine (the same hormone that induces metamorphosis in “normal” amphibians). And when they turn into proper adult salamanders, they suddenly become much poorer regenerators. They can still replace a limb – kind of. But they take twice as long as non-metamorphosed axolotls of the same age and size, and they invariably wind up with small, malformed limbs, often missing bones. After amputation, new skin is slower to grow over their wounds, and the cells that gather under the new skin are sluggish to divide. Something about metamorphosis – that isn’t simply age – dramatically changes how they respond to amputation.

Reference: Monaghan JR et al. (2014) Experimentally induced metamorphosis in axolotls reduces regeneration rate and fidelity. Regeneration advance online publication, doi: 10.1002/reg2.8

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2. Similar cells repair muscles in crustaceans and vertebrates

“Regeneration” can cover a lot of different processes. For example, depending on the creature and the organ you’ve damaged, regenerated body parts can come from totally different kinds of cells. In planarian flatworms, a single kind of stem cell can replace anything else in the body. In the eyes of newts, mature cells of the iris transform into lens cells to replace a missing lens. In our muscles, there are special cells called satellite cells that are held in reserve specifically to make new muscle cells when needed.

This recent study of a little crustacean called Parhyale hawaiensis suggests that muscle regeneration in the fingernail-sized arthropod works in much the same way. Konstantinidis and Averof shot early embryos of Parhyale with DNA encoding a fluorescent marker, which randomly integrated into the genomes of some of the cells it hit. In a few “lucky” individuals, the marker ended up labelling just one cell lineage, and the pair used these animals to figure out which cells made which tissues in a regenerated limb.

It turned out that cells in Parhyale are limited in their potential. Descendants of the ectodermal lineage could make skin and nerves but not muscle, and the mesodermal lineage built muscle but not skin or nerves. Moreover, labelled cells only contributed to regeneration near their original location – animals with their left sides labelled never regrew glowing limbs on the right side. This is starting to sound a lot like vertebrates, but it’s still a very general observation. However, the similarities don’t end there.

Like vertebrate muscles, the muscles of the little crustaceans contain satellite-like cells derived from the mesodermal lineage that sit beside mature muscle cells and express the Pax3/7 gene. When the researchers transplanted some of these cells from animals with the glowy label into leg stumps of non-glowy animals, there were glowing muscle cells in some of the regenerated limbs. So like satellite cells, these cells can turn into muscle during regeneration. There’s little question that muscle cells have a common origin in vertebrates and arthropods like Parhyale, but it’s really cool to see that their mechanisms of regeneration also might.

Reference: Konstantinidis N & Averof M (2014) A common cellular basis for muscle regeneration in arthropods and vertebrates. Science, published online 02/01/2014, doi: 10.1126/science.1243529

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3. Convergent evolution is a poor explanation of rhodopsins

Proteins can be difficult. I mean, sometimes they do their darnedest to hide their family ties. A protein is a chain of amino acids (on average about 300 of them) often folded into a complex shape. Closely related proteins have obviously similar amino acid sequences. However, more distant relatives can be harder to identify. There are about 20 different kinds of amino acids in proteins, so the number of possible sequences is unimaginably vast. The same function can be carried out by very different sequences, and therefore enough evolution can completely erase sequence similarity.

Protein structures are generally thought to be more conserved than sequences. Like function, structure allows for a huge amount of sequence variation without significantly changing. However, theoretically, it’s possible that two unrelated proteins have similar structures because of their similar functions, not because of common ancestry. Apparently, this has been argued for the two types of rhodopsins – proteins that harvest light in systems as different as a the “solar generator” of a salt-loving microbe and the photoreceptors of our own eyes.

If Type I and Type II rhodopsins are similar despite being unrelated, one would assume that this is because they need to be that way to capture light. There are, after all, astronomical numbers of possible protein structures, and the chances of two protein families accidentally stumbling onto the same one without selection steering are slim to say the least. But, in fact, you can rearrange the structure of a rhodopsin in all kinds of cunning ways without destroying its function. This rather weakens the case for convergent evolution, and suggests that similarity of structure does indicate common ancestry here.

Reference: Mackin KA et al. (2014) An empirical test of convergent evolution in rhodopsins. Molecular Biology and Evolution 31:85-95

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4. Starfish can see their way back home

(Blue starfish, the beast featured in the paper, in its natural habitat. Richard Ling, Wiki Commons.)

Starfish aren’t widely known as visual creatures, but they do have eyes at the tips of their arms. The eyes are a bit… basic – no lenses, just a hundred or two little units filled with photoreceptors. Garm and Nilsson set out to find out how the starfish used their eyes. They measured or calculated the eyes’ visual fields (five arm-eyes together can see pretty much everywhere around the animal), resolution (very coarse), reaction speed (slow), and their sensitivity to various wavelengths (they are colour-blind, most sensitive to ocean blue).

Then they took some poor starfish and dumped them a little way off the coral reefs they like staying on. The creatures could walk home from short distances (about 2 m or less), but if you take them too far away, they just wander around in random directions. Likewise if you take off their eyes (don’t worry, they regenerate) or do the experiment in the dark. In conclusion: starfish eyes aren’t exactly top-end cameras, but they are definitely useful to the animals. And what would a slow, brainless mopper-up of coral reef rubbish do with eagle eyes anyway?

(The paper states the walking speed of these starfish as about 4-5 cm per minute. I have a feeling this wasn’t the most exciting fieldwork these guys have done…)

Reference: Garm A & Nilsson D-E (2014) Visual navigation in starfish: first evidence for the use of vision and eyes in starfish. Proceedings of the Royal Society B 281:20133011

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5. What makes wormies settle

OK, Shikuma et al. (2014) one isn’t so much for its own news value, but I hadn’t known that my favourite worms need bacteria to settle until I saw this paper, so I think it deserves a mention. (Besides, it has beautiful pictures of baby Hydroides in it, which I couldn’t resist posting below. They are So. Cute. Yes, I’m weird.)

Shikuma_etal2014-hydroidesBabies

Tubeworms of the serpulid family have swimming larvae which are in many ways like the acorn worm larvae mentioned in my previous post (except cuter). They are tiny, look nothing like an adult worm, have bands of cilia for swimming and feeding, and live in the plankton until they’re ready to metamorphose. When they find a place they like, they settle and turn into adult worms. And apparently, this particular species (Hydroides elegans) not only needs a specific bacterium to like a place, it needs specific proteins produced by that bacterium.

The proteins in question are the components of a nasty device bacteria probably stole from viruses and then used to poke holes in one another. But to Hydroides larvae, they appear to be necessary for metamorphosis. Put healthy bacteria together with worm babies in a dish, and you’ll get happily settled little worms. Do the same with bacteria with damage to the relevant genes, and nothing happens. Use an extract containing the proteins but not the bacteria, and you still get metamorphosing worms. Use too much, though, and they start dying. Everything in moderation…

(Maybe my dismal failure at raising happy young worms years ago could have been remedied with the right bacteria?)

Reference: Shikuma NJ et al. (2014) Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343:529-533

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6. Relative of animals does strange multicellularity with familiar genetics

Although this idea probably hasn’t reached popular perception, animals are surrounded by other multicellular lineages in the tree of life. Sure, most of them are only part-time multicellular, but that’s beside the point. What’s clear is that multicellularity, at least in its simpler forms, is rampant in our extended family. Slime moulds do it, fungi do it, our closest relatives choanoflagellates do it, and our next closest relatives, filastereans and ichthyosporeans also do it.

These latter two groups are really poorly known (the fact that only a taxonomist could like the latter’s name probably doesn’t help), but the situation is getting better with the attention they are receiving as relatives of animals. There are now genome sequences out, and some people are looking at the life cycles of the little creatures to search for clues to our own origins.

Iñaki Ruiz-Trillo recently published a paper describing an ichthyosporean that can form a weird kind of colony with many nuclei in the same membrane starting from a single cell (Suga and Ruiz-Trillo, 2013). Now his team describe a different kind of multicellularity in a filasterean, Capsaspora owczarzaki. Rather than developing from a single cell, this guy does something more akin to the slime mould way: take a load of individual cells and bring them together. (Below: a clump of Capsaspora cells from Sebé-Pedros et al. [2013]. On the right is a regular photograph of the colony. The two-coloured fluorescence on the left indicates that the colony formed by different cells coming together rather than a single cell dividing.)

Sebé-Pedros_etal2013-F4.capsasporaClump

But, interestingly, some of the genetics involved is similar to what animals use, despite the different ways in which the two groups achieve multicellularity. For example, we’ve known since all those genomes came out that the proteins animals use to glue cells together and make them talk to each other are often older than animals. Well, Ruiz-Trillo’s filasterean appears to ramp up the production of some of these when it goes multicellular. It also uses a gene regulation strategy that animals are really big on: it edits the RNA transcribed from many genes in different ways depending on cell type/life stage before it’s translated into protein.

A lot of the details are going to need further investigation, since this was a global RNA-sequencing study with a bird’s-eye view of what genes are doing. It’s still a nice reminder that, like most other innovations in evolutionary history, the multicellularity of animals didn’t spring fully formed out of nowhere.

References:

Suga H & Ruiz-Trillo I (2013) Development of ichthyosporeans sheds light on the origin of metazoan multicellularity. Development 377:284-292

Sebé-Pedros A et al. (2013) Regulated aggregative multicellularity in a close unicellular relative of metazoa. eLife 2:e01287

The use of a larva?

Hi! Long time no see!

(I think we’ve reached the point where it’s weird to say happy new year. I could swear xkcd had a pertinent chart of funny, but I couldn’t find it.)

Once upon a time, I briefly mentioned the problematic relationships of hemichordates. Since a short paper bearing on the subject came out relatively recently (i.e. in December, yes, I’m far behind the times ;)), I thought I’d revisit it.

To begin, let’s orient ourselves on my trusty old animal phylogeny.

animalPhylogeny

Hemichordates are a phylum of deuterostomes, and their closest relatives appear to be echinoderms like starfish. The inside of Deuterostomia looks something like this:

deuterostomes

Hemichordates come in two flavours: the butt-ugly (but nevertheless intriguing) acorn worm, which even the artistic eye of 19th century zoologists couldn’t make appealing (a selection of them from Johann Wilhelm Spengel’s work below):

… and the slightly nicer-looking pterobranch. Well. They’re kind of fluffy. That counts as “nicer,” right? (A couple of Cephalodiscus from the Halanych lab below):

Acorn worms and pterobranchs have different bodies adapted to very different lifestyles. Pterobranchs are stalked, tentacled filter-feeders that often clone themselves into colonies that live together in a branching tube system. Acorn worms are solitary burrowers without tentacles, tubes or shells. Hemichordates possess features in common with vertebrates, such as gill slits, and they seem a lot less freakish than their sister phylum Echinodermata. So hemichordates are kind of the natural go-to group to look for properties of the deuterostome common ancestor.

The only problem is, to do that, you need a solid understanding of hemichordate phylogeny itself. Because there are two very different kinds of hemichordates, you have to first figure out which of those best represents their common ancestor: the sit-at-home plankton sifter or the roaming mud-eating worm. (Maybe neither. Wouldn’t that be funny.) And, as it happens, there’s some disagreement about that.

One view, espoused by the mighty zoological tome of Brusca and Brusca (2002) among others, puts acorn worms and pterobranchs as separate sister groups, and considers pterobranchs the more conservative of the two. The Bruscas write, on page 869, that “the enteropneusts [= acorn worms] have lost [their tentacles], no doubt in connection with their development of an infaunal lifestyle.” In this view, the deuterostome ancestor was a sessile filter feeder, and the long worm-like body and general moving-aboutiness of other deuterostomes is a new feature.

The other hypothesis, backed by DNA sequence data (Cannon et al., 2009)* and more recently the discovery of a tube-dwelling acorn worm from the Cambrian (Caron et al., 2013), is that pterobranchs are a weird subgroup of acorn worms and therefore unlikely to say much about our own distant ancestors.

One thing that AFAIK both camps agree on is that the ancestral acorn worm had a larva that looked nothing like an acorn worm. That’s something pretty common for marine invertebrates. Creatures as different as sea urchins and ragworms explore the seas by way of tiny, planktonic larvae that later metamorphose into a completely different animal**. (Tornaria larva of an unidentified hemichordate below by Alvaro E Migotto from the Cifonauta image database.)

However, the specific family of acorn worms that pterobranchs supposedly come from does not have such a larval stage. They develop more or less directly from fertilised eggs into mini-acorn worms.

Pterobranchs are poorly studied, so not much is known about their babies. Are they like the conventional acorn worm larva, with its distinctive body plan and curly rows of cilia? Or are they more straightforward precursors of the adult, like their presumed closest cousins? Stach (2013) describes a larva of the pterobranch Cephalodiscus gracilis that looks more like the latter. He found the minuscule creature crawling around in a colony of adult Cephalodiscus, and used thin sections and transmission electron microscopy to make a 3D reconstruction of it.

(His account of finding the baby makes me wonder how the hell he knew it did belong to Cephalodiscus. If my experience with tube-dwelling marine invertebrates is anything to go by, being found in a certain animal’s home is no guarantee that you’re related to said animal. I suppose, incomplete though they may be, older descriptions of pterobranch babies were good enough to identify the little guy?)

The image that emerges is of a rather featureless little sausage. According to Stach, it has a through gut, one full-fledged and one partially formed gill opening (asymmetry like that is not unheard of in deuterostome embryos/larvae), as well as a body cavity and a bunch of muscle cells. What it doesn’t have is any trace of the bands of cilia that “typical” acorn worm larvae use to swim and feed, nor some other structures (e.g. nerve centres) that characterise such larvae.

Taken at face value, this would suggest (assuming this is a typical pterobranch larva) that the pterobranchs-are-acorn worms people are right. I have my reservations, and not just because a sample size of one makes me statistically nervous. Using this description as evidence for evolutionary relationships assumes that traditional larvae with ciliary bands are hard to lose. But that’s quite possibly not the case.

Echinoderm larvae, for example, have changed a lot even in the last few million years. The changes occurred many times independently, and often involved a return from a full-fledged larval stage to more direct development (Raff and Byrne, 2006). I don’t know whether acorn worms display a similar sort of flexibility. How many have even been studied in terms of development?

So: detailed internal structure of a pterobranch larva? Cool. As to the worms first hypothesis… “consistent with” would be a better description than “supports”, I think.

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Notes:

*Although microRNAs beg to differ (Peterson et al., 2013).

**The history of these larvae is a mighty can of worms, or trochophores and tornariae as the case may be. I shall say no more on the matter here. 🙂

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References:

Brusca RC & Brusca GJ (2002) Invertebrates (second edition). Sinauer Associates.

Cannon JT et al. (2009) Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts. Molecular Phylogenetics and Evolution 52:17-24

Caron J-B et al. (2013) Tubicolous enteropneusts from the Cambrian period. Nature 495:503-506

Peterson KJ et al. (2013) MicroRNAs support the monophyly of enteropneust hemichordates. Journal of Experimental Zoology B 320:368-374

Raff RA & Byrne M (2006) The active evolutionary lives of echinoderm larvae. Heredity 97:244-252

Stach T (2013) Larval anatomy of the pterobranch Cephalodiscus gracilis supports secondarily derived sessility concordant with molecular phylogenies. Naturwissenschaften 100:1187-1191

Thumbs down, what?

Bird fingers confuse me, but the explanations confuse me more, it seems.

I didn’t mean to post today, but I’ve just read a new review/hypothesis paper about the identities of the stunted little things that pass for fingers in the wings of modern birds. The review part is fine, but I’m not sure I get the difference between the hypothesis Čapek et al. (2013) are proposing and the hypothesis they are trying to replace/improve.

To recap: the basic problem with bird fingers is that fossil, genetic and developmental evidence seem to say different things about them.

1. Fossils: birds pretty clearly come from dinosaurs, and the early dinosaurs we have fossils of have five fingers on their hands with the last two being reduced. Somewhat closer to birds, you get four fingers with #4 vestigial. And the most bird-like theropods have only three fingers, which look most like digits 1, 2 and 3 of your ordinary archosaur. (Although Limusaurus messes with this scheme a bit.)

2. Embryology: in developing limb buds, digits start out as little condensations of tissue, which develop into bits of cartilage and then finger bones. Wing buds develop a short-lived condensation in front of the first digit that actually forms, and another one behind the last “surviving” digit. Taking this at face value, then, the fingers are equivalent to digits 2, 3 and 4.

3. Genetics: In five-fingered limbs, each digit has a characteristic identity in terms of the genes expressed during its formation. The first finger of birds is most like an ordinary thumb, both when you focus on individual genes like members of the HoxD cluster and when you take the entire transcriptome. However, the other two digits have ambiguous transcriptomic identities. That is, bird wings have digit 1 and two weirdos.

Add to this the fact that in other cases of digit loss, number one is normally the first to go and number four stubbornly sticks around to the end, and you can see the headache birds have caused.

So those are the basic facts. The “old” hypothesis that causes the first part of my confusion is called the frame shift hypothesis, which suggests that the ancestors of birds did indeed lose digit 1, as in the digit that came from condensation 1 – but the next three digits adopted the identities of 1-2-3 rather than 2-3-4. (This idea, IMO, can easily leave room for mixed identities – just make it a partial frame shift.)

Čapek et al.’s new one, which they call the thumbs down hypothesis, is supposedly different from this. This is how the paper states the difference:

The FSH postulates an evolutionary event in which a dissociation occurs between the developmental formation of repeated elements (digits) and their subsequent individualization.

versus

According to the TDH no change of identity of a homeotic nature occurs, but only the phenotypic realization of the developmental process is altered due to redirected growth induced by altered tissue topology. Digit identity stays the same. Also the TDH assumes that the patterning of the limb bud, by which the digit primordia are laid down, and their developmental realization, are different developmental modules in the first place.

(Before this, they spent quite a lot of words explaining how the loss of the original thumb could trigger developmental changes that make digit 2 more thumb-like.)

I…. struggle to see the difference. If you’ve (1) moved a structure to a different position, (2) subjected it to the influence of different genes, (3) and turned its morphology into that of another structure, how exactly is that not a change in identity?

Maybe you could say that “an evolutionary event” dissociating digit formation and identity is different from formation and identity being kind of independent from the start, but I checked Wagner and Gauthier’s (1999) original frame shift paper, and I think what they propose is closer to the second idea than the first:

Building on Tabin’s (43) insight, we suggest causal independence between the morphogenetic processes that create successive condensations in the limb bud and the ensuing developmental individualization of those repeated elements as they become the functional fingers in the mature hand, thus permitting an opportunity for some degree of independent evolutionary change.

Am I missing something? I feel a little bit stupid now.

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References:

Čapek D et al. (2013) Thumbs down: a molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology B, published online 29/10/2013, doi: 10.1002/jez.b.22545

Wagner GP and Gauthier JA (1999) 1,2,3 = 2,3,4: A solution to the problem of the homology of the digits in the avian hand. PNAS 96:5111-5116