Crown-of-thorns feed by extending their stomachs on coral colonies to digest the thin layer of soft living tissue covering the coral skeleton. The skeleton thus exposed become a suitable growing surface for algae, and many small invertebrates (worms, shrimps, clams) move in. When alive, coral colonies do not make a good home. Most species cannot deal with the coral’s stinging cells. However, once the crown-of-thorns remove the coral tissue (with its stinging cells), a shrimp or a worm find the coral’s hard skeleton a good place to hide from fish predators. Other species prefer corals when they are alive. That’s particularly the case of butterfly fishes who feed on live corals. So when corals undergo these massive die-offs, butterfly fishes have not much to eat.

In

When it comes to plants, it is not uncommon that a small part is used to regrow a full organism. Gardeners have used this property to multiply and spread varieties of fruits and vegetables for centuries. For many species, a small branch, a leave or a root, placed in the right conditions, will give rise to a fully grown plant that will produce flowers and fruits. The plants obtained by this process are clones of their parents, they have the exact same genetic material. Many species of plants use this mode of reproduction in nature to spread. Because there is no exchange of gametes, this is referred to as asexual reproduction.

In the animal world, asexual reproduction is not very common. As I’ve previously mentioned, a particular group of rotifers have championed asexual reproduction. In other groups, like colonial organisms such as corals, asexual reproduction and growth are tightly linked. The colony grows by adding new individuals. If for some reason, one or a few individuals get separated from the colony, they will be able to go on with their lives and create a new colony of their own. A particular group of flatworms (planarians, class Turbellaria) have the amazing ability to regrow a full adult animal from a single adult cell (you can read more about it here). They use these regenerative abilities to reproduce asexually. They split themselves in halves, and each part regrow what is missing.

For larger and more complex animals, it is however much more uncommon to be able to regenerate the full animal from a part. Echinoderms are an exception. Some sea cucumbers can do it, but the most striking examples come from the sea stars in the genus Linckia. These sea stars can drop off an arm and from it, it will regrow a complete animal.

In the first few days of the expedition here in Papua New Guinea, divers have been bringing back many specimens of Linckia multifora. This colorful sea star comes in shapes that does not match their names. Instead of looking like stars, they often look like comets.

From the “tail” of the comet, the arm that was dropped off, 4 arms are slowly growing back to form a new complete sea star. As the process continues, the little arms grow bigger, and they will eventually end up looking like stars again.

However, the process is not always perfect, and it is often possible to say if a particular individual is the result of asexual reproduction. If you look more closely at this sea star, you can spot that it has 2 anuses (yellow arrows) and 2 madreporites (blue arrows). This is clearly the signature that this individual is the product of asexual reproduction.

Sea stars can probably undergo asexual reproduction more easily than other animals because they have most of their organs repeated in each of their arms. Also, they don’t have a centralized nervous system, it would probably be a trickier thing to do if they also had to regenerate a full brain. Because of the position of their mouth, it is also one of the first thing to be regrown, so they don’t have to starve for too long before they can feed again. If many species of sea stars can regrow a missing arm, only a few can, like Linckia multifora, regrow a full animal from just an arm.

It seemed a little strange that this particular folder was throwing an error message while others did not. I realized it’s because the label “foo” itself didn’t exist in my list of labels. I only had labels nested within it. In other words I had the folders “foo/bar”, “foo/bla” but I didn’t have “foo” by itself. It was working fine before I upgraded never really thought about it much before today.

I created the top level labels in Gmail where needed, and now everything seems to be fine.

You can download the paper here.

This paper is also the occasion to give the species its common Japanese name: the éclair sea cucumber. Look for the figure in the paper .

I also wrote a couple of posts a few months ago concerning this species and why we are studying it in more details.

Holothuria nigralutea. Okinawa. 45m. Dorsal side.

After migrating to Evolution 3, new mails that go directly in folders stopped showing up in Evolution. Further, some of my emails starting to get their labels removed on my Gmail account.

As Evolution 3 stores messages in the maildir format, when you point it out to the folder where offlineimap synchronizes your emails, it starts by creating hidden folders with the same names and moves the current messages in them. So, if you start with a folder called let’s say “Alerts”, evolution will create a folder called “.Alerts”. Your current (“cur”) folder under “Alerts” will be emptied and moved in the “cur” folder under “.Alerts”. The issue with this is that offlineimap interprets that you just removed the “Alerts” label to all your messages.

For the labels that are nested, Evolution actually now follows the maildir standard and use the dot as a separator. For instance, a Gmail labeled called “Alerts/Comments” will become in your maildir folder “.Alerts.Comments”.

Furthermore, if you had a dot in the name of your label, let’s say “2010.Archives”, during the renaming folder process, Evolution 3 will convert this to “.2010_Archives”.

How to fix this and make it work again?

1. First, stop offlineimap to check for your account (cancel the cron job if it’s how you tell offlineimap to check your account).
2. Second delete your ~/.offlineimap folder so that modifications to your maildir folder are not interpreted as labels being removed.
3. Start Evolution 3 and let it do all the renaming and moving around of your messages
4. Close Evolution, delete all the cmeta, index and data files created by Evolution in the maildir directory
5. Delete all the folders that used to contain your messages (after making sure that they’re all empty)
6. Edit your .offlinemaprc file:
   1. change sep=/ to sep=.
   2. change your nametrans line to: nametrans = lambda folder: re.sub('\s+', '', re.sub('(.+)(\\.)(.+)', '\\1_\\3', re.sub('(^.{1})', '.\\1', re.sub('.*Trash$', 'Trash', re.sub('.*Drafts$', 'Drafts', re.sub('.*Sent Mail$', 'Sent', re.sub('.*Starred$', 'Starred', re.sub('.*All Mail$', 'Archive', re.sub('^(INBOX)', ' ', folder)))))))))
   3. This series of regular expressions does the following:
      1. Every folder gets a dot appended in the front. '(^.{1})', '.\\1'
      2. Dots inside your labels are replaced with underscores (you’ll need to change it if you have more than one dot in your labels): '(.+)(\\.)(.+)', '\\1_\\3'
      3. All the Gmail special folders are moved to the root (i.e., “[Gmail]/Trash” becomes “Trash”)
      4. The Inbox folder is moved to the root of your directory. This is done in three steps, first “INBOX” is replaced by a space '^(INBOX)', ' ', then a dot is appended in front (like all the other folders) and the extra trailing space is then deleted '\s+', ''.
7. Restart offlineimap and make sure that everything is working the way it’s supposed to.

The process was a little bumpy but I can now read my emails in Evolution again.

Here you can download the full version of the .offlineimaprc file.

The gray form of Holothuria edulis. Cape Maeda, Okinawa, 15m. Photo by François Michonneau/FLMNH released under CC Atribution

How can a succession of A, T, C and G (the base pairs) help to distinguish between species? Just like you, each cell in the body of a sea cucumber contains DNA that it inherited from its parents when the sperm and the egg fused. To create a fully functional organism based on this single initial cell, the DNA has to be duplicated many times. Because each cell contains its own copy of DNA, the DNA is fully duplicated before each cell division. There are many mechanisms to ensure that the duplicated DNA is a perfect copy. However, on rare occasions, mistakes are made. DNA molecules are large and some parts are more important than others. In parts that are not very important, these mutations can accumulate without many consequences. In important parts, the slightest alteration can have important results. Because of these differences, not all parts of the DNA molecules evolve at the same speed. Some evolve so fast that they are unique to each individual and can be used in forensics to convict or acquit a suspect. Some change so little that they are almost identical across the entire tree of life.

Where mutations happen very rarely, if you find two individuals that share the same one in their DNA, they are more closely related than individuals that don’t have this mistake. In other words, they share the same mistake because at some point in the past, their ancestors had the same parents. In animals cells, there is DNA in two compartments: the nucleus and the mitochondria. In the nucleus, each gene has two copies (one comes from mom, the other from dad) and the genes are arranged in long linear molecules: the chromosomes. The genes in the nucleus are responsible for most of the functions and appearance of the organism. Mitochondria are responsible for converting energy from sugars to make it available to the cells. In each mitochondrion, DNA is stored in a small single circular molecule and only contains genes that are useful to the mitochondrion. Unlike DNA in the nucleus, genes in the mitochondria are found in single copies: mitochondrial DNA from the parents don’t mix, and only the mother contributes. These characteristics make the evolution of mitochondrial DNA easier to track and understand than nuclear DNA.

A typical animal cell showing the location of the nucleus and a mitochondrion. From NCBI.

Within the mitochondrial DNA, a gene has been widely used to help telling species apart. In most organisms, this gene accumulates mutations just at the right speed so that each species has a unique sequence. Because of this feature, the sequence of this gene can be considered as a “barcode”. Just like each product at the supermarket has a unique sequence of numbers represented as a barcode, the sequence of this gene is unique to each species. However, contrary to the barcode that is found on all the packs of your favorite cookies, the barcode found in the mitochondrial DNA of a species is not perfectly identical from one individual to the next. Instead, out of the about 700 letters that make up the barcode, it is common to find a dozen of differences between the two sequences, but it’s rare to find sequences that have more than 35 differences between two individuals of the same species.

Coming back to our species complex, what does the barcoding gene sequences have to say? The two most divergent barcode sequences that we have for the Holothuria edulis complex have about 20 differences, and they both belong to the pink sausage group. What is more surprising, is that the gray ones have exactly the same barcode sequence as some of the pink ones. The éclairs have their own unique sequence. However, they only have about 10 differences with some of the sequences from the pink ones.

If the barcode sequence was a perfect way to tell species apart, it would mean that the three color forms within this species complex are actually all the same species. However, it is not perfect. The three forms could actually be three good biological species that don’t interbreed, and yet, their barcode sequence could say otherwise.

The first explanation to this pattern is these three form became different species very recently. Even when a species doesn’t interbreed with another, it takes many generations for the barcode sequence to be completely unique and characteristic of this species. At first, when a pool of individuals start to diverge from the rest of the population, they will carry with them only a small sample of the barcode sequences that were characteristic of the ancestral population. Generation after generation, some of these sequences will go extinct (because the individuals carrying them didn’t leave any descendants), and others will slowly accumulate mutations. Because these individuals don’t interbreed with the rest of the population, these mutations will become characteristic of this new divergent species.

An alternative explanation could be that these three forms are actually different species but recently they swapped their mitochondrial DNA. In species that recently split, it can happen that the mechanisms preventing different species to interbreed fail. They can hybridize and in the process mix up their DNA, and in particular mitochondrial DNA. If it were the case, the signal shown by the barcode sequence could be misleading. The species may have stopped interbreeding a long time ago, but if they swapped their mitochondrial genes recently, the information from the barcode gene would be make us think that they belong to the same species.

The alternative to these hypotheses could be that the barcode gene is correct: the three forms are actually the same species and they just look different because they live in different habitats for instance.

Schematic reconstruction of what might be happening to the DNA of diverging populations. DNA is represented as a series of colored boxes. Each color represent one type of DNA base. A, B & C represent 3 lineages and each line correspond to a generation. At each generation an individual can leave one (or more) descendant with an identical copy of its DNA (white arrows), a descendant with a modified copy of its DNA (red arrow) or does not leave any descendants (crossed white arrows). At the fourth generation, lineages A & B cannot interbreed with C (represented by the dashed line). However, because of the recent history of their DNA, at the fourth and fifth generations B & C have more similar sequences than A. It would suggest, as in the first explanation, that B & C are more closely related despite the fact they cannot interbreed. Given enough time (generation 6 on the drawing) the lineages would reflect the correct relationships. If all the lineages could interbreed, DNA could still be exchanged. In this case B & C would seem closely related despite a history of reproductive isolation (as in the second explanation).

In the end, we are in a situation where color patterns and ecology say one thing (the three forms are different species) while ossicles and genetics suggest another (the three forms are the same species). Which is right? To understand what is happening in this particular case, in the next months, I am going to look at what nuclear genes have to say about it. Remember, mitochondrial genes only show a small part of the story as they are transferred only through the mothers. Nuclear genes, in particular those accumulating mutations faster than the barcode gene, could help explain what we observed in the mitochondrial DNA, and in turn, help us understand whether the pink sausage, the éclair and the gray one are the same species.

The island of Okinawa is part of the Ryukyu Islands, an archipelago in southern Japan.

For marine biologists, it is a very interesting place. First, the island is big enough to have lots of different types of habitats. Because many species are really picky about the place they call home, more kinds of habitats means more species are likely to be found. Second, Okinawa is at the northern limit of the Indo-West Pacific, the largest and most diverse marine biogeographic region.

The main goal of my visit was to collect specimens belonging to a species complex of sea cucumbers, and along the way compiling the list of all species of sea cucumbers that inhabit Okinawa.

The species complex I’m studying is called Holothuria edulis. In most areas of the Indo-Pacific, Holothuria edulis is easily identifiable. And for good reasons. It looks like a pink sausage that is burnt on one side. It prefers shallow places (less than 10 m / 30 ft) that are a little silty with few waves. That’s why it is usually very common in lagoons and back-reefs. It’s active both during the day and at night.

Holothuria edulis (the pink sausage). Photo by François Michonneau/FLMNH. CC.

In 2007, Mark O’Loughlin published with some other eminent sea cucumber biologists a new species that they named Holothuria nigralutea. The specimens were collected in Western Australia between 90 and 100 m (300 to 330 ft). At a first glance, it doesn’t look very similar to the pink sausage Holothuria edulis. It is almost twice as long, it is light yellow with a series of black blotches on the dorsal side and a black stripe on the ventral side.

Holothuria nigralutea (the éclair). Dorsal view. Photo by François Michonneau/FLMNH. CC.

Holothuria nigralutea (the éclair). Ventral view. Photo by François Michonneau/FLMNH. CC.

To tell species apart, sea cucumber biologists like to look at ossicles. They are microscopic “bone”-like structures that are found in the skin of sea cucumbers. They can take all kinds of shapes and usually each species of sea cucumber is characterized by a unique set of ossicles. However, the ossicles of Holothuria nigralutea look very similar to the ones of Holothuria edulis.

Ossicles from Holothuria nigralutea (left) and Holothuria edulis (right). Fron O’Loughlin et al 2007.

So, last year while in Okinawa, we were very surprised and excited when one of our hosts, Daisuke Uyeno, brought us back 3 specimens of Holothuria nigralutea from his 45 m (145 ft) dive. Not only was it very far away from the location the species was first seen, but it was also much shallower. This considerably changed what we thought we knew about this species.

In Japan, biologists often give common names to species so that they can refer to them easily in Japanese. For Holothuria nigralutea the common name is “ekureanamako” or the éclair sea cucumber. Indeed, the black stripe on the ventral side of this species just looks like the delicious pastry.

An éclair by CraZeeCrafteeZ, on Flickr. CC.

After the pink sausage and the éclair, let me introduce you to the third player: the gray one. It likes the clear waters of the fore reefs exposed to waves. It is found usually below 10 m (30 ft) but not much deeper. It is a nocturnal beast. During the day it hides in crevices, but when the sun goes down it mops the reef frenetically (as much as a sea cucumber can be). It is also very easy to recognize: the dorsal side is taupe gray with white speckles while the ventral side is light beige. The gray one is found in some places of the Western Pacific: Micronesia, Cooks Islands, New Caledonia, Nauru and Okinawa. The gray one doesn’t have a scientific name. Indeed, there is no physical difference other than the coloration that can tease this species apart from the pink Holothuria edulis.

The gray one. Photo by François Michonneau/FLMNH. CC.

To summarize we have three very different looking animals: the pink sausage, the éclair and the gray one. They are very different sizes: about 15 cm (6 in) for the pink one, 30 cm (12 in) for the gray one and 45 cm (18 in) for the éclair. They live in different places: shallow lagoons for the pink, exposed reef slopes for the gray one, and much deeper for the éclair. Yet, their anatomy is very similar and their ossicles are almost identical. So despite their apparent ecological differences, are they all the same species?

In the next post, we’ll see what the DNA has to say about it.

Sources & Credits:
- P. Mark O’Loughlin, Gustav Paulay, Didier Vandenspiegel and Yves Samyn (2007). New Holothuria species from Australia (Echinodermata: Holothuroidea: Holothuriidae), with comments on the origin of deep and cool holothuriids. Memoirs of Museum Victoria. 64: 35-52. link | PDF
- All sea cucumber pictures by François Michonneau/FLMNH licensed under Creative Commons Attribution.
- Eclair picture by CraZeeCrafteeZ on Flickr licensed under Creative Commons BY-NC-ND.

This is really useful for instance to figure out what a fish eats. By sequencing the DNA found in its gut, and by matching it against the database of known DNA sequences, it becomes possible to determine what is its favorite food.

Another application is for identifying larvae. For many marine animals, life starts as a larva which might look totally different from the adult. However, both the larva and the adult share the same DNA so if we know the DNA of the adult, we can figure out how the larva looks like. Compare the larva and the adult for this species of crab (Xanthias lamarcki). Hsiu, a post-doc in our lab, works on this project.

To learn more, you can read the full article, browse the photo gallery or explore the infinite photo.