It is the age-old question that has stumped the finest minds for thousands of years. [...]]]>

News sites left and right are picking up a story that “Scientists solved the chicken or egg problem”. Google News aggregated 164 news articles at the time of writing, with more being added every minute. The typical introduction runs like this:

It is the age-old question that has stumped the finest minds for thousands of years. But scientists claim to have finally discovered the answer to the conundrum of what came first – the chicken or the egg?
~Daily Express

Humanity would be in trouble indeed if its ‘finest minds’ are troubled by trivial questions like this! The articles go on to vaguely describe a particular protein that is involved in egg shell formation. While this is certainly interesting, it’s got little to do with chicken evolution or the famous chicken-or-egg ‘problem’. I tracked down the original publication and first online coverage to find out what went wrong here.

The 'who came first' question is trivial at best.

The original paper appeared over a month ago in a chemical journal of the German Chemical Society. It’s a nice study that describes how the carbon carbonate crystals that make up egg shells are formed. The British researched applied molecular modeling to calcium carbonate crystallization in the presence chicken protein ovocleidin-17 (OC-17).

Normally, small amorphous nanoparticles of calcium carbonate molecules don’t crystallize well because the energy barrier for the transition to the more stable crystalline phase is large. However, when OC-17 binds and coordinates the calcium carbonate particles with its arginine residues (described as a ‘clamp’), the energy barrier largely disappears and the calcium carbonate happily crystallizes. When the crystallizing particle starts growing, OC-17 detaches again. The whole mechanism Freeman and colleagues propose really is quite nice.

Ovocleidin-17 coordinates the carbon carbonate particles with its argenine residues, inducing crystallization.

The first online appearance of the story is in this press release of the University of Warwick. I have to admit, the press release really does cover the research pretty well. Of course it ends with some vague promises for crystallization and material science, but otherwise it is a fairly balanced piece. To spice up the article, the press writer decides to include an innocent reference to the famous ‘chicken or egg’ riddle:

The work may also give a partial answer to the age old question “what came first the chicken or the egg?” The answer to the question in this context is “chicken” or – at least a particular chicken protein.
~Warwick University press release

The anonymous writer is careful enough (“partial answer”, “in this context”), but merely being careful is never enough on the internet… The yolk really hits the fan when mainstream news stories pick up on this press release, with metro being one of the main champions of misinterpretation. The following quote from first author Colin Freeman doesn’t help much:

‘It had long been suspected that the egg came first but now we have the scientific proof that shows that in fact the chicken came first,’ said Dr Colin Freeman, from Sheffield University, who worked with counterparts at Warwick University.
~Metro

After the Metro story launched, other mainstream news sites jumped on the bandwagon for a ride. It’s funny and sad to see the whole story turn into a game of Chinese Whispers. ‘Ovocleidin-17′ becomes ‘vocledidin-17′ on Fox News. On various news sites, the study of OC-17 gets reduced to a single sentence. The resulting article doesn’t make sense any more and has become confusing as hell.

Luckily, many readers are smarter than the science ‘journalists’ that have mindlessly copied and pasted this story:

What a silly article. This finding does not “prove” that the chicken came first. After all, if the first chicken did not come from an egg, it was not a chicken. All this really says is that a protein was identified which controls eggshell formation.
… What overblown sensationalist reporting…
~Gabriel on Metro

I didn’t exactly hold mainstream science journalism in high esteem, but I’m amazed that science journalists continue ‘covering’ science stories in this way, even when readers are calling them out. While the trouble may have started with a misleading introduction and a quirky quote, it is the journalist’s responsibility to check facts and put a story into a context. Coverage like this does more harm than good for the public image of science reporting and scientists themselves:

Another brilliant revelation from the British scientific community, but could the tens of millions of pounds of taxpayers’ money that they receive in research grants not be used to discover something of value like the discovery of a new source of cheap, clean energy!
~David, on Metro

Luckily we’ve still got Wikipedia to guide us when we’re misguided and confused:

Wikipedia entry for "Chicken or the Egg"

Oh, wait a minute…

You might not think much of sponges. Maybe you feel that they’re only good for rubbing your back and cleaning your kitchen sink. While you’re absolutely right that sponges have to be admired for their absorbing qualities, they have much more to offer this world. Like on the front of early animal evolution: [...]]]>

You might not think much of sponges. Maybe you feel that they’re only good for rubbing your back and cleaning your kitchen sink. While you’re absolutely right that sponges have to be admired for their absorbing qualities, they have much more to offer this world. Like on the front of early animal evolution: new research by a Croatian team of scientists shows that these simple creatures harbour a genomic complexity that matches our own!

Sponges really are pretty cool animals. As an example, Henry van Peters Wilson discovered the regenerative abilities of sponges in 1907: after putting a living sponge through a sieve, fragmenting its cells in this way, he saw that the remaining clumps of cells found each other again to form what he called ‘plasmodial masses’. After a while, complete sponges emerged again from these ‘masses’!

This remarkable regenerative flexibility might partly reflect the transition that their ancestors underwent from a colonial to a multicellular species (scientists believe sponges evolved from colonies of protozoans much like Monosiga brevicollis). Sponges can lay claim to being the first animals on this planet, and the common ancestor of all animals might very well have been a very sponge-like critter.

Spongia officinalis, or "kitchen sponge". It is dark grey because it is alive, unlike the dried out yellow one in your bathtub. Source.

Sponges are morphologically not very complex. They depend on the flow of water to obtain food and oxygen and remove their waste products. Their porous body structure and skeleton are built to optimize this flow of water, making it flow through all interconnected chambers. Sponges have a number of different cell types, with some that can generate the water flow with their beating flagella, some that can contract and transmit signals like muscle cells and others that maintain and repair the sponge ‘skeleton’.

Such a simple animal must have a pretty simple genome right? Not exactly. Matija Harcet and colleagues sequenced a large set of expressed genes from two different sponges and compared them to their homologs from sea anemone , sea squirt , nematode , fruit fly, sea urchin and human. As you can see in the phylogenetic tree below, the sponges (porifera) occupy a basal position on the tree of metazoans. Consider the surprise when most sponge gene transcripts mapped back to the human and sea anemone proteomes, whereas nematodes and fruit flies ranked the lowest on the list!

Phylogenetic relationships between sponges (porifera) and other animals. We humans are hiding within "Chordata", sea squirts within "Tunicata" and sea urchins in "Echinodermata".

Moreover, the sponge transcripts not only matched the most genes in sea anemones and humans, the protein sequences were also much more similar to human genes than those of other species. You can see this for yourself in the beautiful figure below. Every dot is a transcript that is placed closest to the species it is most similar to. The sponge transcripts most often fall in the human or sea anemone (N. vectensis) quadrants.

A possible explanation for this observation could be that genes have been evolving slowly in both sponges and humans, whereas the proteins of nematodes and drosophila have been evolving in overdrive. Since these species have much shorter generation times and larger population sizes, they can acquire mutations at a much higher rate, speeding up the sequence evolution of their genes.

Each dot is an EST plotted at the appropriate relative sequence distance from the other species.

The team also compared the sponge gene repertoire to that of our closest unicellular nephew: the Monosiga brevicollis that was mentioned before. They found more than a thousand genes which were unique to sponges, of which most are predicted to be involved in signalling pathways and cel adhesion processes. This would mean that most gene expansions and genomic innovations that are found in animals today, were already present in the Urmetazoan ancestor of all animals.

Whatever in happened in that great-great grandmother of animals, it was enough to spawn the whole breadth of animals of the Cambrian explosion and those that live today. Sometimes, simple appearances hold complex and fascinating stories. Not bad, for a ‘simple’ sponge!

For those of you unfamiliar with the concept of a blog carnival: a carnival [...]]]>

I’m happy to tell you that molecular and cellular biology bloggers soon will have their own Blog Carnival! The MolBio Carnival came into existence thanks to the joint efforts of Alejandro Montenegro, Lab Rat, Psi Wavefunction, Alexander Knoll and myself.

For those of you unfamiliar with the concept of a blog carnival: a carnival is like a monthly digest of the blogosphere concerning a particular subject. Any blogger can submit their blogposts on the subject of molecular or cellular biology to the carnival hosts. The first Monday of every month, one of the hosts will shortly describe and link to the posts that have been submitted that month.

If you’ve written a blogpost on the subject of molecular or cellular biology, you’re very welcome to submit your posts to the blog carnival online here. From the Carnival description:

This carnival focuses on cellular and molecular biology in different systems: the discussion of peer-review articles, techniques, book reviews and related topics, are all welcomed. Specific areas of interest include, but are not limited to: structure and function of proteins, nucleic acids and other macromolecules, gene expression and its regulation, signal transduction, apoptosis, developmental biology, cell cycle and cell growth, microbiology, biochemistry, structural biology, membrane dynamics and many others. Systems and synthetic biology-related posts are also welcomed.

A blog carnival is a great way of exposing a larger and interested audience to your writing, so spread the word via twitter, e-mails, friendfeed etcetera. The first carnival will be published on the second of August, so waste no time submitting your blogposts! We look forward to receiving your contributions!

In my high school text books, bacteria were primarily defined in terms of what they were not. “Bacteria don’t have a nucleus”, “bacteria don’t have mitochondria”, “bacteria are not capable of complex membrane trafficking” and so on. But such boundaries seem to blur as more and more “eukaryote specific” properties pop up in [...]]]>

In my high school text books, bacteria were primarily defined in terms of what they were not. “Bacteria don’t have a nucleus”, “bacteria don’t have mitochondria”, “bacteria are not capable of complex membrane trafficking” and so on. But such boundaries seem to blur as more and more “eukaryote specific” properties pop up in some corners of the prokaryotic world, with bacterial endocytosis being the latest discovery. The simple finding that some bacteria can ‘eat’ the same way as your and my cells do, could have huge implications for our understanding of the evolution of eukaryotes.

To understand what is so special about endocytosis in bacteria, we’ll first have to take a look at what bacteria normally do and don’t do. If a bacterium wants to take up particles from its surroundings, it does so in non-specific ways.  Small molecules or peptides can be taken up passively via channels in the membrane, or actively via importing ‘pumps’. Normal proteins are far too big to be taken up in this way, so the only way bacteria can gobble up a protein is if it’s completely smashed to bits (by proteases for example).

Eukaryotes have more sophisticated importing mechanisms, allowing them to import molecules as large as entire proteins. When eukaryotic receptors sense a protein the cell wants to import, Part of its cell wall invaginates as membrane coat proteins line the newly formed pit. The invagination gets deeper and deeper until the membrane closes and an internal vessicle is formed.  This vesicle now contains part of the extracellular fluid and any (macro)molecules that where floating around at the time. The vesicle can now be internalized for further processing in the endosomes. The entire process is known as endocytosis, which you can see beautifully animated using electron microscropy pictures in the video below.

A while ago I wrote a guest post on Lab Rat’s blog on the discovery of typical eukaryotic membrane coat proteins in some bacteria. This finding of compartments and membrane coat proteins in the bacterial branch of Planctomycetes was suspicious of course: do these bacteria actually use all this machinery for endocytosis? A month ago, the exciting answer was published in PNAS with one of the most simple and elegant experiments I have seen in a long time. To show that the Planctomycete Gemmata obscuriglobus (literally ‘strange ball’) is taking up proteins via endocytosis, Lonhienne  and colleagues incubated the bacteria with green fluorescent protein. Within 5 minutes of incubation the cells were glowing like christmas trees, proving that the bacteria had taken up the complete protein! A normal bacterium would cleave the GFP to bits and pieces, and import the remaining peptides into the cell. There’s no way the GFP would still be fluorescent if Gemmata had taken up the GFP in this way. In other words, Gemmata carefully took in the light bulbs it found on its doorstep, whereas other bacteria would first smash them before dragging in the pieces.

When incubated together with fluorescent proteins (GFP), Gemmata obsuriglobus happily gobbled it up and started glowing!

The next step was looking where the fluorescent proteins ended up. In eukaryotes, a specific organelle called the endosome is the first stop for endocytosed proteins. From there it is decided whether the protein will be degraded, returned to the membrane or passed on for further processing in the Golgi apparatus. The team labeled the GFP proteins in the cell with little gold particles, so that  they would show up as distinct black spots on electron microscopy pictures. As you can see in the picture below, most of the proteins are localized in a special compartment: the paryphoplasm, which seems to be an expansion of the bacterial periplasm. The authors discovered that proteins got degraded in this paryphoplasm. Moreover, the team found invaginations and vesicle like structures within the cell that are normally associated with endocytocis. That certainly sounds like complex membrane trafficking to me!

Most GFP proteins (little black dots) localize to the paryphoplasm (marked with "P").

So where does that leave us? Endocytosis, comparmentalization and membrane sorting are no longer exclusive to eukaryotes. This could mean that the entire endocytosis machinery evolved before the latest eukaryotic ancestor did. If this is what happened, we would expect to find the system conserved and retained in a few bacterial phyla, such as the planctomycetes. Bacteria in this phylum have other ‘strange’ and eukaryote-like properties (for a bacterium at least): they reproduce via budding, surround their genetic material with membranes, synthesize sterols and don’t have peptiodglycan in their cell walls. The origin of eukaryotes may well lie with an ancestor that has many of the properties planctomycetes have today. If it’s true that planctomycetes are the prokaryotes most closely related to eukaryotes, Carl Woese’s famous tree of 1991 may need to be redrawn. That would be about time too, because that thing is getting close to ancient for a field that is moving so quickly as evolutionary biology! It’s interesting to note that this scenario of eukaryotic evolution is also in direct conflict with the hypothesis that eukaryotes arose after the endosymbiosis of an archaeon by a bacterium, so expect to see some fireworks as experts debate how to integrate these findings into our current understanding of evolution..

I’m not an expert on eukaryotic evolution, but I can tell you that the discovery of a bacterium with so many distinct ‘eukaryotic’ features will impact on our ideas and views of the history of life on this planet. Before the dust settles, the song “Take it in” by Hot Chip strikes me as wonderfully appropriate:

If coral reefs are the rain forests of the tropical oceans, kelp forests are the woodlands of the Northern seas. Kelp is one of the algal species that can survive the harsh conditions of the North Sea that I know and love, together with other hardy seaweeds like bladder wrack. All these seaweeds [...]]]>

If coral reefs are the rain forests of the tropical oceans, kelp forests are the woodlands of the Northern seas. Kelp is one of the algal species that can survive the harsh conditions of the North Sea that I know and love, together with other hardy seaweeds like bladder wrack. All these seaweeds are part of the larger family of the  brown algae, which are generally good at dealing with unfavorable conditions, such as large fluctuations in light, temperature and salinity. The evolutionary past of Brown Algae is particularly interesting, as it is assumed that they arose via the fusion of two eukaryotes (their chloroplasts have four membranes)!

The first brown algal genome sequences will be entered in sequence databases soon, since scientists published the Ectocarpus genome in Nature a few weeks ago. As the first representative of brown algae, Ectocarpus has the honour of joining the ranks of giant pandas and body lice in having its genome sequenced, promising exciting insights in how multicellularity can evolve.

Kelp blowing in the "wind" in Diamond Bay. Kelp forests are one of the most productive ecosystems of temperate and cooler seas. Source: saspotato on Flickr

The genome is of course rich in interesting nuggets of molecular insights into biological observations. For example, brown algae are known to have some strange polysacharides in their cell walls, such as alginates, which give seaweeds their gummy feeling. The genes involved in the biosynthesis of alginates were first described in bacteria, but the brown algal genes have were never identified. Now with the Ectocarpus genome in hand, the researchers still couldn’t find any homologs of the bacterial genes. This probably means that brown algae independently evolved enzymes to synthesize these funny polysacharides. Whatever biological problem arises, evolution will find a (different) way!

The Ectocarpus genome is also rich in genes dedicated to harvesting light in fluctuating conditions, containing 53 light harvesting complex genes. What’s more, the team found an enzyme (DPOR) that can synthesize chlorophyll in dim light or in the dark. The DPOR enzyme cannot be find in many terrestrial plants, and seems to be more commonly found in green algae.

On to the real interesting stuff. Brown algae are one of the few clades that can lay claim to inventing multicellularity. Because contrary to what simple overviews of evolution tell you, the emergence of multicellular life wasn’t a single ‘big leap’ in the evolution of life on earth. ‘Multicellular leaps’ occurred in at least five different branches of the tree of life: the metazoans (animals), fungi, green algae / plants, red algae and brown algae.

The place of brown algae and Ectocarpus within eukaryotes. All five multicellular lineages have been coloured, with brown algae unsurprisingly in brown and us metazoans in funky blue.

In an attempt to explain why certain species became multicellular, the authors analyzed the total gains and losses of gene families in separate lineages. I’m not a big fan of this approach, it reeks a bit of the ‘the deflated ego problem’ where we assume that ‘complexer organisms’ must have more genes than ‘less complex’ lineages. To support their statement that ‘multicellular organisms have lost fewer gene families and evolved more new gene families than unicellular lineages’, they predicted the gains and losses of different gene families in some eukaryotic lineages (below). I am not really convinced: Ectocarpus and Laccaria seem to fall within the range of half of the unicellular lineages analyzed. The authors themselves have to admit that they fail to detect significant trends.

The gains and losses of gene families in different lineages of eukaryotes.

The authors however do find several gene families that could have contributed to developing multicellularity. Of particular interest are the integrins, that are not found in other stramenopile genomes (Oomycetes and Diatoms in the phylogeny above). In animals integrins are vital for ‘sticking’ cells together, so it’s easy to see why they would be important for other multicellular organisms. The team also found many ion channels that are unique to animals, including the IP3 receptor. This receptor plays a central role in the very fast calcium signaling, which animal cells use to quickly react to stimuli (it is used in muscle contraction, for example).

This typical combination of metazoan and algal genes in the Ectocarpus genome reflects its interesting evolutionary past, where two eukaryotes fused to give rise to a successful lineage. Considering the many genes derived from algae , the chimera maybe arose from a photosynthetic algal-like eukaryote and a (heterotrophic?) eukaryote that is closer to the metazoan lineage. Consider the identity crisis the poor guy must have faced! Luckily, by keeping the right sets of genes and ditching the obsolete ones, the brown algae overcame this crisis and blossomed into a rich and diverse branch on the tree of life.

This is the first blogpost in a continuing series on “sensible evolution‘: how our senses evolved and shape the way we see the world. We perceive everything that we can see and feel as ‘real’, but we know that our human senses only capture a tiny part of the natural world. There are [...]]]>

This is the first blogpost in a continuing series on “sensible evolution‘: how our senses evolved and shape the way we see the world. We perceive everything that we can see and feel as ‘real’, but we know that our human senses only capture a tiny part of the natural world. There are other realities out there. At least, we seem to have a richer taste palette than some of our animal cousins, including the mythical vampire bat..

Tasteful mechanisms
Having ‘good taste’ is not only necessary to gain the approval of ‘high society’ – it also vital for survival in many animal species. Bitter or sour tastes can warn you that a certain food source contains toxins or is otherwise harmful, while a salty taste indicates the food is rich in minerals. Sweet and umami tastes hint at the presence of carbohydrates and proteins – telling you this piece of food is likely nutritious. Special taste receptor cells on the tongue are responsible for detecting the tastes, but they don’t recognize each taste equally. Sour and salty tastes are detected via ion channels, whereas bitter, sweet and umami are recognized by GPCRs.

Animals display a huge variation in bitter taste receptors, since what is toxic for some animals, can be nutritional for others. Rats have twice as much different bitter taste receptors (42) as dogs (21), for example. There’s not that many ways to recognize sweet and umami though. The Tas1r1 (umami) and Tas1r2 (sweet) proteins both team up with Tas1r3 as heterodimers to form the functional taste receptors, as in the figure below.

Tas1r3 heterodimerizes with Tas1r1 or Tas1r2 to form sweet or umami taste receptors. Tas2rs are the bitter receptors and don't dimerize.

Sweet evolution
Some species seem to get by without tasting sweetness or umami at all. The Giant Panda has an inactive umami Tas1r1 and cats have their sweet Tas1r2 pseudogenized, for example. These losses might be driven by changes in diet (with the panda being an extreme example – going from being a carnivore to living off bamboo), but without closely related relatives with different dietary lifestyles to compare them to this is difficult to say.

Studying bats, which have a more recent history of diversification and lifestyle changes, might be more fruitful. Most bats either are insectivores or fruitivores. However, three bat species chose the more sinister sanguivorous way of life. They are the only mammals that exclusively feed on the blood of other animals. Thirty years ago, researchers already discovered vampire bats have little interest in sugar. Now, Zhao and colleagues sequenced the Tas1r2 gene in 40 different bat species to find out more about the evolution of sweet taste perception.

Vampire bats, cool like that. Source: http://www.casadosmorcegos.org

They reconstructed the gene tree of Tas1r2 with maximum likelhood methods and found that Tas1r2 was under strong purifying selection in both insectivores and fruitivores, meaning that for these species there’s a strong evolutionary pressure to keep the sweet taste receptor intact and functional. However, in all three vampire bats the Tas1r2 gene was disrupted in different ways. The damage included nonsense mutations, insertions and deletions and make the entire sweet taste receptor non-functional. Such a non-functional gene will not get eliminated from the genome immediately. Instead the sequence of such a pseudogene will slowly deteriorate over time, until it lost all resemblance to the gene of the protein it once coded for. The researchers show that the selection pressure on Tas1r2 has likely been lifted in the common ancestor of vampire bats, and has been evolving neutrally ever since.

Since vampire bats find their prey by smell and infrared vision and exclusively feed on blood, they seem to have little need for refined tastes. Any myths about vampires preferring sweet blood can thus be dispelled: these poor suckers (literally) will not enjoy glucose rich blood more than blood-light products!

The Tas1r2 gene is also inactivated or deleted in chickens, zebra finches, horses, the western claw frog and cats. There’s not a clear relationship between diet and selection/retention of Tas1r2, since all these animals prefer different food sources and not all of them had dramatic life style switches like the vampire bat. The chicken and zebra finch case is interesting because they are only distant cousins, implying that sweet taste perception either was lost in the common ancestor of birds, or that it was lost multiple times.

I guess in this respect, we primates are just lucky! I wouldn’t even want to know how stroopwafels would taste like without my beloved Tas1r2 gene!

Last week’s blog post on the ancestry of the malarial plasmid attracted several insightful comments by Psi Wavefunction. One of the issues discussed was when exactly the malarial ancestor changed his lifestyle from being a coral symbiont to a coral parasite. This week I came across a paper in PNAS that shows [...]]]>

Last week’s blog post on the ancestry of the malarial plasmid attracted several insightful comments by Psi Wavefunction. One of the issues discussed was when exactly the malarial ancestor changed his lifestyle from being a coral symbiont to a coral parasite. This week I came across a paper in PNAS that shows that corals themselves also have an interesting evolutionary story to tell about switching lifestyles!

Two lifestyles
Corals come in all kind of sizes, shapes and (fluorescent) colours. But almost all of them can broadly be divided into two separate lifestyles. First up are the loners. These corals, like the sun coral below, prefer a nocturnal lifestyle . They capture prey with the tentacles that extend from the polyps. The word “Prey” means different things for different coral species, as it can range from feeding on zooplankton to digesting entire shrimps, or even fish!

The solitary (and appropriately nicknamed) sun coral Tubastrea Faulkneri.

The second walk of life is the ‘social’ one. These corals are social in more than one way. Firstly, they don’t seem to mind crowds since many of them form colonies. When a young larval coral of this type has found a nice place to settle, it spawns other polyps via asexual budding. The polyps then integrate into a single colony by removing the skeletal barriers between them. The other social aspect of these corals is that they live in symbiosis with zooxanthella, which function as little energy factories for the corals by trapping light from the sun and converting it into energy via photosynthesis.

Because of this symbiotic relationship with zooxanthella, symbiotic corals have to live in shallow waters. The corals receive huge benefits from the symbiosis, receiving orders of magnitude more energy than their heterotrophic nephews. However, the heterotrophic solitary corals can be found in much wider distributions and at much greater depths than their symbiotic peers, because they’re not restricted to the photic zone.

Coral Clades
The differences between the two different lifestyle are pretty dramatic. Consider the confusion when scientists discovered that several different clades of closely related corals contained both solitary and colonial members! No matter how you’re going to spin it, this either implies that coloniality evolved multiple times, or that it was lost multiple times during coral evolution.

If you’ve got a progressive view of evolution (which you shouldn’t) you might think that corals have evolved from the solitary single polyps, into the ‘complexer’ colonial forms that share nutrients and have colony-wide regenerative responses. A recent publication in PNAS shows that different scenario is more likely and (I think) way more interesting.

To find a consensus phylogenetic tree, Barbeitos and colleagues used Bayesian inference methods. They also used Bayesian analyses to reconstruct the possible lifestyles of ancestral corals and to estimate all possible transition rates (e.g. how likely it is that a symbiotic coral becomes solitary).

The consensus coral phylogeny obtained by Barbeitos et al. Open/closed squares stand for asymbiotic/symbiotic corals, open/closed circles stand for solitary/colonial corals.

Coral evolution
Their results are pretty conclusive: their models rarely showed solitary corals gaining coloniality. Since many of the reconstructed ancestors are colonial and symbiotic, the authors find that coloniality was lost at least 4 times in different coral clades, while symbiosis was lost at least 1 time. From these results it’s hard to say whether coloniality or symbiosis was preferentially lost first. Since some facultative symbiotic corals exist, it seems relatively easy for corals to lose the symbiosis. For losing coloniality, the researchers also provide an interesting explanation: heterochrony, of which neoteny is a special form.

Heterochrony seems to be one of the main drivers of phenotypic evolution and is pretty easy to understand if you realise that developmental changes underlie phenotypic changes most of the time. A small change in the embryonal stage can have big effects for the mature organism. However, evolution is not a magical inventor that makes new structures or life stages spring into existence. What evolution can do is tinker or interfere with what’s there already. By delaying maturation, organisms can become sexually mature even in their larval/juvenile forms! This could similarly have worked the ancestor of solitary corals, where the asexual expansion phase is terminated and an earlier sexual maturation of the corals. The observation that many solitary corals still have the capability (even if they don’t do so in the wild) to reproduce asexually seems to support this hypothesis!

Neotenous to the extreme. The mental and physical qualities of mature chihuahuas seem to match those of unborn wolves. Seriously, what

So where does that leave us with the evolutionary history of corals? If we put together the facts that a) the distribution of symbiotic corals is limited to depths where light can penetrate and b) deep-water solitary corals evolved from symbiotic and colonial corals, it’s safe to conclude that the shallow waters and reefs of the past were the evolutionary cradles from which all extant corals evolved. The robust loners can trace back their ancestry to the more social, but also more fragile, symbiotic corals. Nowadays, coral reefs still sustain some of the richest biodiversity on this planet. Their fragility and current rapid destruction should worry us, as the authors gloomily conclude:

The potential disappearance of tropical reefs in the next century could have evolutionary consequences for Scleractinia and other taxa that may span eons to come.

Let’s make this clear from the start, I don’t like the term “living fossils” at all. It’s as if we decided that certain species are second class organisms that should have gone extinct a long time ago. Unfortunately for me, the term regularly crops up in the popular scientific press. Especially [...]]]>

… except in Hollywood movies.

Let’s make this clear from the start, I don’t like the term “living fossils” at all. It’s as if we decided that certain species are second class organisms that should have gone extinct a long time ago. Unfortunately for me, the term regularly crops up in the popular scientific press. Especially the BBC seems to have a particular affinity for the concept. Even worse, scientific literature is polluted with this muddy term now and again¹. Why would that be a problem? Because the term makes absolutely no evolutionary or scientific sense at all.

Ben Stiller is the only human known to have encountered a real living fossil. Unfortunately for Mr Stiller, of all the ammonites, ground sloths and trilobites that populate the fossil record, he had the bad luck to walk into a T. Rex.

There are many reasons people refer to extant organisms as living fossils. They are all bullocks. Let’s go through the list.

1. Living fossils have been around for billions/millions of years and have changed little over time.

Even the morphologically most constant species will change and diverge over time. The horseshoe crab, the poster child of ‘living fossils’, can make this insightful.

It is true that the first recognizable horseshoe crabs make their first appearance in the fossil record around ~445 million years ago. But based on these fossilized shells alone, paleontologists can already recognize dozens of different horseshoe crab species that lived in the past, in addition to the four different species of horseshoe crabs alive today. In fact, the extant Atlantic horseshoe crab doesn’t show up in the fossil record at all!

So the horseshoe crabs that live today did NOT exist millions of years ago. Furthermore, the only part of the horseshoe crab that fossilizes well is its shell, so we know almost nothing about the soft tissues of ancient horseshoe crabs. Any information about particular physiological organization of organs or genomic differences is lost forever. Fossil horseshoe crabs maybe would be more recognizable as different species if we DID had access to that information. If anything, genetic drift will have made sure that the genetic composition of an ancestral horseshoe crab and an extant one are fully incompatible as millions of years passed. In other words, while it would make a cool experiment, trying to cross a ‘modern’ horseshoe crab with one of its ancestors will most likely fail.

The horseshoe crab, while sporting an impressive pedigree, is NOT a 'living fossil'.

Continuing with the completely arbitrary list of properties that define a living fossil (partly taken from this awful wikipedia page):

2. Living fossils… have all survived major extinction events

Newsflash: the ancestors of EVERY organism alive today have experienced ‘major extinction events’. That’s sort of why we’re here today.. This kind of reasoning can take completely ridiculous forms, as in the case of the Cypriot mouse².

“All other endemic mammals of Mediterranean islands died out following the arrival of man, with the exception of two species of shrew. The new mouse of Cyprus is the only endemic rodent still alive, and as such can be considered as a living fossil,” said Dr. Cucchi.

The Cypriot mouse diverged approximately half a million years ago from its fellow mice and continued to evolve, adapting to the Cypriot island and drifting away from their mainland nephews. So does the status of sole survivor of an extinction event make the Cypriot mouse a living fossil? Humans are the only surviving members of the genus Homo, but we don’t go about calling ourselves living fossils now do we?

The cypriot mouse. Cute, but not a living fossil.

3. A species which successfully radiates … has become too successful to be considered a “living fossil”

If you needed any reason to regard “living fossils” as complete bullcrap, this is it. “Successful radiation”?? How on earth can that be measured? For all we know, ‘living fossils’ may have ‘successfully’ radiated in the past, even if few species in that clade survive today. This definition also implies that species can lose their “living fossil” status if they diverge further in the future, making it a pretty worthless biological concept.

As an example. both Coelacanths and Elephantidae are genera that spanned dozens of species in the past. So subjectively, we could think of them both as ‘succesful’ groups of species. However, extinctions eliminated all but two species in both Elephantidae and Coelacantha. Yet, coelacanths are viewed as ‘living fossils’ whereas elephants are apparently alive and kicking! If that’s not arbitrary, I don’t know what is.

The list of living fossils on wikipedia has no biological relevance at all. The troubles the wikipedians have in getting a clear definition of what constitutes a living fossil really says enough. To me it looks like a half baked attempt to provide some kind of psuedoscientific justification for branding some species as ‘primitive’. Of course, the usual victims such as the highly derived platypuses and crocodiles feature on the list. Guess what: as Jonathan Eisen pointed out earlier, there are no ‘primitive’ species. Or ‘living fossils’ for that matter.

So please, spread the word, and whack people on the head with a fossilized trilobite if they ever use the word ‘living fossil’.

This post was partly inspired by this question asked on the very cool website ask a biologist.

1.Amemiya, C., Powers, T., Prohaska, S., Grimwood, J., Schmutz, J., Dickson, M., Miyake, T., Schoenborn, M., Myers, R., Ruddle, F., & Stadler, P. (2010). Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome Proceedings of the National Academy of Sciences, 107 (8), 3622-3627 DOI: 10.1073/pnas.0914312107

2. T. CUCCHI , A. ORTH, J.-C. AUFFRAY , S. RENAUD , L. FABRE, J. CATALAN, E. HADJISTERKOTIS, F. BONHOMME & J.-D. VIGNE (2006). A new endemic species of the subgenus Mus (Rodentia, Mammalia) on the Island of Cyprus Zootaxa