Ants, DNA Barcoding and Open Access

This week, as Alex Wild put it, Brian Fisher and Alex Smith "break the PLoS taxonomy barrier". In my last post, I evangelized and pontificated on the benefits of open access publishing in PLoS for taxonomy. That in itself is a ground-breaking accomplishment, but the paper by Fisher and Smith is interesting in own right. They report on ants in the Malagasy region from 2 genera, Anochetus and Odontomachus, and describe 3 species new to science. Additionally they evaluate the efficacy of DNA Barcoding as a "tool to accelerate species identification and description".

Of Ants and Islands

Madagascar is a unique island off the eastern coast of Africa with a highly endemic fauna, meaning that many of the creatures found there are found no where else on this planet. Fisher and Smith also report the first records from the nearby islands of Seychelles and Comoros. Using 500 individuals from 6,000 leaf litter samples, 4,000 pitfall traps, and 8,000 additional hand collecting events over a 14 years period, they were able to group together worker, queen and male castes. The descriptions are fine and document the features and variation in morphology well. One criticism I have is they contain no information that I could see on the etymology of the new species. Etymology is where the author describes what the name means. For the 3 new species described in the genus Anochetus, each is given a specific epithet honoring an individual, a Mr./Ms. Bolton, Goodman and Patterson. Who these people are that should get immortalized in ants we shall never know.

DNA Barcoding and Species Assessment

While the description and discussion on the ants' distributions are important for biodiversity studies, the authors spend a good deal of the paper discussing the efficacy of DNA barcoding in helping to delineate taxa. DNA barcoding is using a standard gene, typically the mitochondrial COI gene, as a marker to identify a species. This is useful when there is a specimen voucher with a known barcoded sequence to match unknown to. There is a good deal of controversy surrounding its use in taxonomy. Many taxonomists agree that describing species based only on a short snippet of DNA is bad practice.

Fisher and Smith use DNA barcoding on their ants for two reasons. The first is group the different castes together. Ants are social insects separated into workers, queens and males. Some ant societies have even more castes, such as sanitary workers and fungal farmers. Because the different ant castes are morphologically different from one another, it is sometimes difficult to tell closely related species apart, especially if they co-occur in a similar location. The authors assert that DNA barcoding was the "principal source of data" that group together different castes, sizes and genders.

The other reason is to rapidly assess species identification. Fisher and Smith analyzed all the collections of a genus. Those showing a high degree of sequence divergence, i.e. the outliers, were "culled" from the analysis for morphological scrutiny. Traditionally, each individual would have to have measurements and notes taken on the morphological characters of interest. This is an extremely time-consuming process, but amplify that to 500 individuals of ants. The barcode method actually allowed them find the interesting individuals right away. This might not work for every taxon, but considering how affordable DNA sequencing has become this practice might take off for large collections. This will be extremely important as many biodiversity inventories are ongoing or coming to a close in the near future.

Another use for DNA barcoding brought up by Fisher and Smith is hypothesis generation. Hopefully most people will agree me (and the study's authors) that species are testable hypotheses. Like any scientific hypothesis, it is subject to refinement with new data. The barcode data helped Fisher and Smith to generate testable hypotheses regarding within-species divergence, several interesting aspects of biogeography (see page 20, last paragraph of first column for list) and female-limited dispersal capabilities in species with wingless queens.

I'll let Fisher and Smith have the final word:

"Nothing can replace the countless hours of careful observation necessary to understand variation and to delimit species boundaries. However, the addition of sequence data provides a means to create short-term results from inventories and at the same time generate data helpful to taxonomists. For taxonomists, sequencing highlights the specimens most deserving of focused study."

Disclaimer: Brian Fisher was my Evolution teaching assistant at UC-Davis. Although he is unlikely to remember me anyways, but the contents of this post are not in any way an artifact of this coincidence.
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Fisher, B.L. & Smith, M.A. (2008). A Revision of Malagasy Species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae). PLoS ONE, 3(5), e1787. DOI: 10.1371/journal.pone.0001787

Taxing Taxonomy Top 10

Another top ten featuring inverts was recently posted by Christopher at the Catalogue of Organisms - his top ten phylogenetically problematic taxa. I guess this is a good list to have a strong showing of inverts in, but then again?

7 out of 10 are inverts including one of my favorites - Pycnogonida.

Gotta check out the complete list including why they are so challenging to taxonomy. 

Quote of the Day

"The discrepancy between the histories of populations and the histories of genes within those populations is the biggest problem afflicting the phylogenetics species concepts."
- Coyne, J. A., & H. A. Orr. 2004, Speciation. Sunderland, Sinauer Associates, Inc.

Hey English Majors!

How do you cite a translation of a text? Do I include the original author followed by the translators, all as authors, and the year of the translation?

For instance what I want to cite is Hennig (1966). But I have and use a translation (from German) of his text. So do I ignore the translators and go with the traditional

Hennig, W. (1966). Phylogenetic Systematics. University of Illinois Press, Urbana. (i've seen this is an article)

or

Hennig, W., D.D. Davis, R. Zangerl (1999). Phylogenetic Systematics. University of Illinois Press, Urbana.

Firefly Double Whammy: Evolution and Costs of Light

Um... no, not that firefly, although suspenders should totally make a comeback... NOT! How about this one:

Photo from Encyclopaedia Britannica.
Author's note: Fireflies will always hold a special place in my heart. Every summer when I was kid I would sit outside in Iowa and watch them, collecting them in my hands so I could peek inside with one eye to see if the lightning bug (as we called them in Midwest) was flashing. I look forward even more now to the day when my children can stay up late enough to watch and collect fireflies themselves. This post is dedicated to my beautiful swedish wife, who discovered fireflies for the first time when we moved east out of California 3 years ago. It is so great to see how excited she gets when they come out each summer!

Fireflies are considered all part of the family of beetles called Lampyridae. Appropriately, this means light. The luminescence is the result of a chemical reaction with the substrate Luciferin and the enzyme Luciferase. The happens in two steps and is energetically expensive (i.e. requires ATP and oxygen). This is a slow reaction, which is why we can see it decay after the initial flash, that is controlled in specialized organ in its abdomen, called the lantern naturally. It sometimes is mistakingly thought of as a bacterial symbiosis like in many marine organisms, but for fireflies (along with many other bioluminescent critters) this is purely a chemical phenomenon.

There are about 2000 species of Lampyrids globally, with about 120 of those in North America. Stanger-Hall et al. recently reported the first phylogeny of North American fireflies in the journal Molecular Evolution and Phylogenetics. Their study also has interesting results for the evolution of light signals in this family. First the basics though, which also have importnat implications. They used nuclear (18S) and mitochondrial genes (16S and COI) to form consensus trees of 27 species of North American fireflies from 17 genera, including one species and genus that was recently placed outside of the family Lampyridae (Pterotus). They found that, in fact, North American fireflies do not form a monophyletic group. This lends support to the hypothesis that firefly diversity has been helped by multiple invasions. Furthermore, they determined that the present taxonomic classification into subfamilies and tribes is not supported by the molecular data, while Pterotus and another genus placed outside of the family are actually nested within the Lampyridae.

Figure 1 from Stanger-Hall et al. 2007. Carbon dust drawings done by Laura Line.
The real interesting result of this study has to do with evolution of the signaling. Branham & Wenzel (2003) report that lampyrid larvae possess of constant, but faint glow in larval light organs on the abdomen. These authors suggest, based morphological character analysis, that light production evolved early, predating the Lampyridae, and was retained from the larval form. This is supported by observational evidence that adults vary widely in light production and light organ placement and use. Typically, lampyrids use their light displays as sexual signals to attract a mate. But more basal family members use pheromones. Citing a chapter by Lloyd (1997), Stanger-Hall et al. describe 3 mating signal systems in the 120 North American species of firefly:

(1) Chemical signals (pheromones): ‘‘dark fireflies’’ (e.g. Ellychnia, Pyropyga, Lucidota) produce no light as adults and are active during the day; they release chemical signals to attract mates. (2) Glows (continuous light signals): ‘‘glowworm fireflies’’ (e.g. Microphotus, Phausis, Pleotomodes) tend to have larvae-like females who spend the day in underground burrows and emerge at night, emitting a continuous glow. This glow (short distance) in combination with pheromones (long distance) attracts males who will fly towards the glow, but usually do not signal themselves. (3) Flashes (short intermittent light signals): ‘‘lightningbug fireflies’’ (e.g. Photinus, Photuris, Pyractomena) are the most commonly observed. They are active at dusk or in the dark and both males and females use species-specific light signals to communicate with each other in an interactive visual morse-code that identifies the species and the sex of the signaler. Some genera (e.g. Pleotomus) and individual species within genera (e.g. Phausis reticulata) may represent intermediate stages in signal evolution (e.g. Pleotomus males glow when disturbed).

In terms of the evolution of signaling, they found no clear patterns. Whether they used flashes, glows or pheromones all the species in the phylogenetic tree were intermingled.
If you click on the above figures from Stanger-Hall et al., you can view them larger but at this size the take-home message is clear. The tree on the top is color-coded by sexual signal modes. Green signifies flashes, orange is glow, grey means using pheromones and weak glows, while black is only pheromones. It is obvious that glows and flashes have multiple origins in the North American firefly fauna.

The tree on the bottom is the same tree, but this time orange branches are for both flashes and glows and black branches are for pheromones only. The asterisks denoted light signal origins (orange) or losses (black) while the letters A & B represent two possible evolutionary scenarios.

"Scenario A, light signals originated once in ancestral adult lampyrids, and were subsequently lost nine times. Scenario B, ancestral lampyrids used pheromones as sexual signal, and the transition to sexual light signals evolved four times independently, followed by four losses. There are at least two other possible 10-step scenarios (multiple gains and losses), but neither is favored by any weighting where losses are considered as likely or more likely than gains. The color-coding of the branches reflects scenario B."

Video firefly larva from Thailand. Note the constant glowing in the posterior segment.
This all provides evidence that supports the hypothesis that the lampyid fauna of North America has invaded the continent multiple times with multiple origins (i.e. Europe or Asia). While scenario A allows for only a single origin of light production followed by 9 losses, scenario B is more parsimonious - requiring fewer steps. It seems to me, and I think there are papers out there that might back it up, that new gains or more rarer than losses. It would be interesting to see a meta-analysis of studies that combined morphology and molecular character data to study if indeed parsimony won out over intuition. If anyone knows of such studies, drop me a line.

Another study published in American Naturalist last month by Woods et al. 2007 studied the energetic costs and the risk of predation associated light production. This video that I couldn't figure out how to embed (might need subscriber access) describes their research (contributed by the authors as additional material with their paper). They measured energetic costs using open flow respirometry, which measures carbon dioxide production, during flashes and when at rest. They found that individual fireflies did have a significant increase in metabolic rate during light production compared to being at rest, but it was less than the rate when they were walking and not flashing. To test the hypothesis that maintaining just the bioluminescent capability has energetic costs, they also tested two other lampyrid species that are diurnal and do not produce light. Standardizing for body, they found no significant differences in the metabolic rate of lampyrids that are capable of producing light and those that have no such capability.

The next step was to see if light production incurred any costs in terms of increased predation. Woods et al. 2007 set up a experiment with arrays of sticky-trap cups with flashing LEDs that simulated the mating signals of Photinus greeni and sticky-trap cups without any light (Figure 1b from Woods et al. 2007, left). P. greeni is chemically defended against would-be predators by synthesizing steroidal pyrones. But there is one predator that is unbothered by this defense and in fact sequesters the compound for use in its own defense. This is another species of firefly called Photuris versicolor that hunts Photinus species by tracking their mating signals and captuing grounded males in the midst of getting it in on. In fact out 218 individuals of Photuris trapped, only 4 were caught on non-flashing traps! Interestingly, 96% of all trapped Photuris were females.

The take home message? Its not energetically expensive to make flash your stuff but you'll attract the wrong company at times!

"Every single night, male fireflies are out there flying a fine line between sex and death. For us, it definitely rivals the most exciting television thriller! So, next time you're outside on a summer night take a moment to admire the firefly romance and risk that’s playing out all around you."-Sara Lewis, Professor of Biology at Tufts University (quoted from press release on physorg.com)

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Branham, M.A., J.W. Wenzel (2003). The origin of photic behavior and the evolution of sexual communication in fireflies (Coleoptera: Lampyridae). Cladistics 19(1), 1–22. doi:10.1111/j.1096-0031.2003.tb00404.x

Lloyd, J.E. (1997). Firefly mating ecology, selection and evolution. In: Choe, J.C., Crespi, B.J. (Eds.), Evolution of Mating Systems in Insects and Arachnids. Cambridge University Press, London, pp. 184–192.

Stanger-Hall, K.F., J.E. Lloyd, D.M. Hillis. (2007) Phylogeny of North American fireflies (Coleoptera: Lampyridae): Implications for the evolution of light signals. Molecular Phylogenetics and Evolution, 45, 33-49. doi:10.1016/j.ympev.2007.05.013

Woods Jr., W. A., H. Hendrickson, J. Mason, S.M. Lewis. (2007) Energy and predation costs of firefly courtship signals. American Naturalist, 170, 702-708.

Monday Midnight Must-Reads

Here are some great posts from the blogosphere that I don't have time to do posts on myself.

First, Christopher Taylor at the Catalogue of Organisms beat me to it. He did a great job reviewing the recent PLoS ONE paper revealing how Acoels are not flatworms. In my ongoing efforts to battle paraphyletic nomenclature, Acoels shall not longer be called flatworms or "acoel flatworms". Find out where they fit at the Catalogue for an in-depth analysis of the paper.

Second, the LiveScience blog posts on new research published in Pain 'N the ASs on the evolution of body size in beetles. While palaeo-beetles were huge, modern-day beetles are pretty small by comparison. This study reports that

"bigger beetle species devote a larger portion of their bodies, proportionately, to airways than do smaller species. And the air passageways that lead from the body core to the legs turn out to be bottlenecks that limit how much oxygen can be delivered to the extremities."-Alex Kaiser, study lead author

Third, awesome song, awesome song lyrics

"There's nothing so pure as the kindness of an atheist

simple act of unselfishness that never has to be repaid 

And there's nothing so sure as a razor blade above your wrist

When you think you just can't stand it
That you're gonna leave empty handed

Do you still dream of being saved"-Freakwater's Gone to Stay from their Old Paint album

It's a beautiful song that is worth the $0.99 on iTunes (where you preview 30sec. of the song too). I found the chords for it and will cover it this week and add it to my list of insurgent country music.

Squid Double Whammy! Synonymy and Humboldt Squid's Range Expansion Fuels Taco del Mar's Squid Tacos

This is what it looks like when two genera are the same genus. Wakabayashi et al. published a paper in the Journal of the Marine Biological Association of the U.K. this month providing molecular evidence, as well developmental evidence, for the synonymy of two genera, Moroteuthis and Onykia. Apparently someone had the observation that Onykia might an immature stage of Moroteuthis (which is large, see picture below). The authors tested this by collecting paralarvae, a small planktonic phase of cephalopods, north of Hawai'i and corroborating morphological analysis with sequence data from the COI gene. The tree above is a good representation of what it should look like when two genera are one and the same. You see them intermingling in the branches. Onykia has nomenclatural precedence so all species under Moroteuthis are now Onykia. Priority is another way of saying first published first served. The oldest date always has priority when synonymzing taxa.

This is an example of a good straight-forward synonymy using data from morphology and genes. Corroboration is the wave of the future man. You can't get rid of morphology, its too damn cool, and you can't ignore genetics, it makes too much damn sense. So what do you do? Use total evidence in understanding phylogeny. Morphological characters have a genetic basis. We don't have the genomes sequenced of every living thing on earth. So can we use morphology as a proxy for genetic divergence? To do so we have to convince ourselves that a morphological trait is shared with other species that are closely related to it. This makes more sense on a lower taxonomic scale such as species, genus or sometimes even family level. For instance, anatomical structures like isopod mouth parts or shrimp legs are easier to group on shared ancestry than say numbers of ass hairs. Variation in the latter is much greater between individuals that between species, while variation in the former may be less between individuals than between species or genera. Modifications in the phenotype are based on changes in the genotype. Since we don't know a priori what gene to sequence to understand the evolution of shrimp legs (called pereopods by the way), we can use the morphological character as a proxy for the genetic evolution. Corroborating these results against gene trees provides powerful evidence.

It's 1 am so I might have to reread what i just wrote in the morning to make sense of it all...

Squid wrestling is a popular pastime on NOAA ships. The wrestler has the former Moroteuthis robusta in a tentacle club lock and is trying to explain to squid that it is now Onykia robusta. Photo courtesy of NOAA Alaskan Fisheries Center.

In other squid news, the mighty Humboldt Squid, Dosidicus gigas, is invading California! Taco del Mar will be offering squid tacos en masse. Craig at Deep Sea News recently posted on a study tracking the range expansion of the Humboldt into California's water. Today, the study came out in PNAS, authored by Zeidberg & Robison. This is a 16-year video time-series of beautiful, scenic and constantly overcast Monterey Bay.

"Climate-related changes in fish distribution have been typically characterized as range shifts or displacement away from the center of the home range, as temperatures grew warmer. In contrast, Dosidicus has enlarged its distribution without abandoning its historical center."-Zeidberg & Robison 2007

The authors correlated squid appearance with loss of Hake. Hake rebounded in years where the Humboldt was absent from surveys. Additionally squid abundance in Monterey Bay is positively correlated with increase in the sea surface temperature of the tropical Pacific (used as a measure of the El Nino effect). But the authors warn,

"The expansion of Dosidicus’ range does not appear to be directly linked to a regional increase in sea-surface temperatures. Although its tropical center of distribution and the El Nino-linked episodic range expansions suggest a warm-water affinity, its vertical distribution in the water column demonstrates a physiological tolerance for temperatures far lower than it encounters near the surface."-Zeidberg & Robison 2007

The authors also made an interesting point that the expansion may in part be due to loss of the Humboldts predators, namely tuna and billfish. Being freed from the constraints of predation, the Humboldt physiological plasticity and rapid growth rate enable it to expand into new habitats quickly. So the negative effect of tuna loss has the positive effect of more calimari rings and squid tacos!

Humboldt squid that had washed ashore in Pebble Beach were stacked with ice on a picnic table to preserve them. The squid have huge eyes to help them hunt in deep, dark waters. Photo: The Carmel Pine Cone, October 10, 2003. From SIMoN.

What the hell is a chaetognath?! Part 3: Epilogue

I started this series because I really wanted to know more about Chaetognaths. I've never run into them in any samples I've collected nor have any real experience with them at all. This may be the reason for my fascination of them. After reading the 2 articles from Current Biology that I discussed in Part 1 and Part 2, I have certainly developed an appreciation of their evolution and Chaetognaths as organisms in the general sense. That is where this post comes in. In that same issue of Current Biology, there is - believe it or not - a third article on Chaetognaths by Ball & Miller. This paper discusses more of the biology of chaetognaths and why they just plain cool creatures.

Eognathacantha ercainella described from 520 million year old rock in China by Chen & Huang 2002
They are a relic of the Cambrian and fossils show that not much has changed in their body plan (above).

"The chaetognaths are an ancient lineage of invertebrates that shares some characteristics with just about every other major invertebrate phylum and has consequently puzzled taxonomists ever since its original description in 1769. Darwin described chaetognaths as ‘‘remarkable for the obscurity of their affinities’’ and they have puzzled a succession of eminent zoologists ever since. Though unfamiliar to most biologists, chaetognaths are typically the most abundant planktonic predators, sometimes accounting for more than 10% of zooplankton biomass and being outnumbered only by their major prey, the copepods."-Ball & Miller 2006

Chaetognaths feed on copepods by sensing their vibrations and are able hunters in darkness (click here for a movie of a chaetognath hunting!). Some even have a neurotoxic venom. They are also simultaneous hermaphrodites. One species, Paraspadella gotoi, exhibits interesting mating behavior with ritualistic dance before exchanging sperm packet(below).
I found it interesting to that the authors note the nervous system bears a resemblance to nematodes, kinorhynchs and priapulids. In the phylogenetic papers of Matus et al. 2006 (see Part 1) and Marlétaz et al. 2006 (see Part 2), the authors take out priapulids from the analyses because they didn't like that Chaetognaths grouped with them within the Ecdysozoa. The Ecdysozoa clade is supposed to encompass the moulting animals. So Chaetognath's nervous system resembles members of the Ecdysozoa AND Chaetognaths have a cuticle. To my knowledge, animal cuticles get shed periodically? I'm not entirely certain if this is true or not, but something to think about. Another thing to about are a priori assumptions, such as we would like Chaetognaths to be closely allied to the Deuterostomes yet have some affinity with Protostomes too. You can't have your cake and eat it to. I think if you are going to use a consensus tree from dozens of genes, you should use the taxa possible/applicable to the analysis. In this case, all animal phyla because the question related to a phylum's position in the phylogeny of the animals.

I have no doubt from the molecular work shown to date that chaetognaths align with protostomes. But the protostomes are a HUGE group encompassing some of the most diverse animal taxa such as the arthropods, molluscs and annelids. Where they fit in that tree means alot evolutionarily. There are alot of biologists that outright reject the Ecdysozoa hypothesis for a variety of reasons. Libbie Hyman, who wrote book(s) on invertebrate diversity quite literally, recognized the affinities of the Chaetognaths to the protostomes:

‘‘It seems probable that the chaetognaths should be regarded as having diverged at an early stage from the primitive ancestor of the Bilateria.’’-Quoted in Ball & Miller 2006

But Chaetognaths aren't the only unresolved taxon. There are many minor taxa which have few people working on them. Some taxa don't even have anyone in the U.S. as a specialist working on that group. Many of these taxa are in desperate need of study and revision and can potentially fill in alot of holes in animal phylogeny.

Photo taken from here
More Chaeognath Stuff:
Erik Thuesen's Chaetognath Webpage
PZ Myers Chaetognath Friday Blogging (2004)

Porifera Double Whammy! Huge Silicate Spicules (or are you just happy to see me?) and the Evolution of Calcification!

Craig at Deep Sea News posted on new research about a deep sea sponge, Monorhaphis chuni (Hexactinellida), with the world's largest known biosilica structure! This is a silcate spicule that can grow up to 3 meters long. Thats at least a meter longer than you!

Picture is copyright Emily S. Damstra and used by permission.
I don't really know how to construe to enormity of that structure. I could make it so you have to scroll down this post 3 meters, but that would just be annoying. The study Craig is referring to on DSN is by Müller et al., published in the most recent issue of Cell and Tissue Research. The authors carefully studied the formation of these giganto-spicules and helped along the way with silicatein-related proteins. Silica is not a common element in the ocean, though rare at the surface it increases in concentration as you go deeper by about 10-fold. The ability scavenge this rare element and incorporate into a biostructure in itself is a feat, and an expensive one at that! Now multiply that over time to about 3 meters...

This study is an excellent exercise in integrative biology. It merges biochemistry, histology, genetics, morphology and systematics. They determined there were different chemical layers to the spicules, including collagen and the silicateins (potentially a first for the Hexactinellida). The conclusion:

"Based on the data gathered here, we suggest that, in the Hexactinellida, the growth of the spicules is mediated by silicatein or by a silicatein-related protein, with the orientation of biosilica deposition being controlled by lectin and collagen."-Müller et al.

Keeping with the theme of sponge skeletons, but moving away from silica-based to carbonate-based, a study by Jackson et al. in June 29 issue of Science used an approach called Paleogenomics to determine the role of precursor alpha-Carbonic Anhydrases (a-CA's) in calcareous skeleton formation. Paleogenomics uses modern techniques, such as gene and protein expression and phylogenetics, on extant organisms in combination with knowledge of their evolutionary history. a-CA's have evolved through several gene duplication events in the Metazoa for a variety of physiological purposes:

"The chemical reaction [CO2 + H2O ⇆ HCO3− + H+] functions in processing metabolic wastes, regulating pH, fixing carbon, and transporting ions across organic membranes. The metalloenzyme carbonic anhydrase is pivotal to these processes by catalyzing this reaction approximately 1 million fold."-Jackson et al.

"(D-F) Spherulite calcification begins with an ovoid structure, with subsequent stages increasing in size. Scale bars, 5 mm." Reproduced from Jackson et al.
A very important enzyme with a diverse set of functions cascading down throughout the Metazoa. The aim of this paper, in my opinion was to see what a-CA's looked like in the last common ancestor to the Metazoa (LCAM). Sponge genomes are great to look at for these types of questions because of their basal position on the animal tree of life. They determined the a-CA enzyme is used in biocalcification of the Demosponges. The sponges (and presumably biocalcification) radiated in the Cambrian Explosion, 520-540- million years ago. The LCAM most likely used the a-CA enzyme for a similar purpose. And in fact we see this feature, biocalcification, presevered in several protostome and deuterostome taxa. As with any well written Science paper, there is a succinct final paragraph concluding their results:

"From our data we infer that a core molecular toolkit capable of catalyzing the production of HCO3− (and ultimately CaCO3) was present in the first metazoans and included an a-CA. Subsequently, various metazoan lineages inherited this toolkit and have added to and elaborated upon its key elements to guide, enhance, and inhibit the deposition of CaCO3 in the spectacular variety of ways we see today."-Jackson et al.

Two well-written sponge papers with important evolutionary conclusions. What more could you ask for?

See also a perspective written by Taylor et al. on how sponges are providing insights into animal evolution.

What the hell is a chaetognath?! Part 2

In Part 1 of What the Hell is a Chaetognath?! we learned from a study by Matus et al. using a consensus tree built from many genes, that Chaetognaths are the sister-taxon to the protostomes. This was surprising because Chaetognaths have long been classified as deuterostomes. The molecular evidence is strong even if I bitched about a few technicalities in their tree-building process (i.e. exluding taxa to get a different tree). A complimentary study in the same issue directly after the Matus et al. article, Marlétaz et al. consider the phylogeny of the Cheatognaths... again.

Before I delve into the science, a bit of an aside. Both studies analyzed genes of Chaetognaths and BLASTed the database of model organisms with those genes (mostly expressed sequence tags or ESTs). Each study had a different set of authors (no overlap) and came to the same conclusion, namely that Chaetognaths are protostomes. That is fine, I think the science is there. But 2 2-page articles saying the same thing with essentially the same method, published in the same issue of the same journal!? Come on people, lets work together. This is a little ridiculous. My guess it is political. One group found out what the other was doing. So as not to step on anyone's toes, they make an agreement to publish together, but separately. It happens. Just a little pointless is all.

Back to science! The Marlétaz et al. paper actually did find something new and interesting though. They sequences over 11,000 ESTs of a juvenile Chaetognath (Spadella cephaloptera, below).

Photo by J.M. Cavanihac from the Chaetognath Tree of Life Project, copyright BIODIDAC

In their prodding around they found the gene for Guanidinoacetate N-methyltransferase. This gene is interesting because it is only found in Deuterostomes and Cnidarians, lost in the Protostomes. It catalyzes the final step towards creatine synthesis, which is an important compound in energy metabolism of brain and muscle. Interesting that this is derived from a Cnidarian ancestor! Maybe that is why our brains look like jelly? Anyways, this provides striking evidence for their placement as a sister taxon to the Protostomes. Hence the common ancestor is not between a Protostome and Deuterostome, but between a Chaetognath and a deuterostome. May I remind you that Chaetognaths share the same embryological characteristics as Deuterostomes, plus now a Deuterostome-specific gene carried down from the Cnidarians and lost to the Protostomes. The phylogeny below (reprinted here without permission) from the Marlétaz et al. paper says it all.


Problems? Well, like I mentioned in Part 1, they exclude the Platyhelminthes from analysis. What is about flatworms that confuses Chaetognath phylogeny?? For one, they were the previous occupants of the sister-clade-to-Protostomes position, otherwise known as the position between Cnidarians and protostomes. Figure S2 from the online supplementary material shows the effects of this analysis. Fig. S2A includes Chaetognaths, while Fig S2B excludes them (reprinted without permission).



As you can see, Platyhelminthes was excluded based on the weak bootstrap support either way. This begs the question about why are Chaetognaths and Platyhelminthes so closely related (potentially), while only Chaetognaths retain deuterostomy characteristics? Thats another topic for another day though. I'll leave you with the concluding sentences:

"It confirms, on a genomic basis, that deuterostomy in an embryological sense is not a decisive character for the classification of animals. Some animals, like the chaetognaths, can be protostomes and yet show features of a deuterostome-like embryology. Nevertheless, the position of chaetognaths as a sistergroup of protostomes prompts us to propose that their development could be reminiscent of the bilaterian ancestor and testify that chaetognaths are a landmark phylum for addressing hypotheses about the origins of bilaterians."

What the hell is a chaetognath?! Part 1

So I thought they were deuterostomes, but apparently thats only half the story. Lynn Margulis classified the arrow worms as deuterostomes in her 5-kingdom classfication (after Whittaker). Their deuterostome characteristics include radial, indeterminate cleavage, a posterior position of the blastopore (deuterostomy), enterocoelous coelom formation and a tripartite adult body plan with a post-anal tail. At least this is what I was taught "growing up". Three papers in Current Biology last year showed that while they have developmental patterns like deuterostomes, their genes tell another story!

The first paper by Matus et al. sampled several phyla and used several genes. A consensus tree built from 72 EST genes grouped them within the Lophotrochozoa. They also constructed a tree using tropomyosin genes showing Chaetognaths as the sister taxon to all the Lophotrochozoa. One thing that bugged about the EST tree is that when they included the Priapulida, Chaetognaths grouped with them in the Ecdysozoa. When the data were reanalyzed without the Priapulids, Chaetognaths grouped with the last common ancestor of the molluscs and annelids. The authors argued that

"The association with the Ecdysozoa, therefore, depends on a single taxon and is not likely to reflect a general affinity for the group."

But shouldn't you use total evidence? Can you really justify leaving out data because it doesn't fit your expectations? In their supplementary material, they show three trees with three different conclusions.
The first tree:

"Bayesian tree based on the analysis of RY-coded concatenated SSU and LSU rRNA genes shows a relationship between the chaetognaths Paraspadella and Sagitta with priapulids."

Conclusion: Chaetognaths are sister-taxon to Priapulids, well situated within the Ecdysozoa.

The second tree:

"Bayseian analysis of Ribosomal SSU and LSU data, excluding priapulids from RY re-coded data... The maximum likelihood bootstrap tree had very low support values."

Conclusion: Chaetognaths are sister-taxon to Platyhelminthes, well situated within the Lophotrochozoa.

The third tree:

"Bayesian analysis of Ribosomal SSU and LSU data excluding long branch platyhelminths and priapulids from RY re-coded data."

Conclusion: Chaetognaths are sister-taxon to all the Lophotrochozoa, occupying a basal position to the clade. This is the tree they liked and went with for their main article.



Don't get me wrong, I (think) I believe them. Their maximum likelihood studies show best support for Tree #3 and fits nicely into a story, keeps everything monophyletic and stable. For instance they state:

"To eliminate long branch attraction artefacts, we analyzed subsets of taxa to determine the effects of taxon sampling (Supplemental data). Regardless of the taxa removed (nematodes, platyhelminths or tardigrades) the chaetognaths remained as sister to annelids and molluscs with varying degrees of support in Bayesian analyses and as sister to the Ecdysozoa (arthropods, nematodes and tardigrades) with weak bootstrap support in likelihood analyses."

I (think) I believe their analysis and conclusions, but I'm just concerned about the structure of the tree. There are profound evolutionary differences between protostomes and deuterostomes or between Lophotrochozoans and Ecdysozoans. One day I will go into detail about the different clades. Either way, the molecular data say Chaetognaths are definitely Protostomes. It disturbs me though that most of the developmental and morphological similarities to deuterostomes, as the authors stated, may be the result of convergent evoluton. In my opinion, convergent evolution tends to destabilize tree topology by decreasing parsimony. Sometimes I feel that when you invoke convergent evolution too much you might as well through up your hands and proclaim the magnificence of the grand designer...

Cnidarian Double Whammy: Anemone Genome Completed and a Worm Thats a Jelly!

Its been a long time in the making and I know everyone is as excited as I am that the first cnidarian genome is finished! This is monumental for cnidarian biologists (such as I sometimes fancy myself to be). The lucky species is Nematostella vectensis (its pimp name is the starlet sea anemone),a small edwardsiid anemone quickly becoming a model organism in developmental biology and now comparative genomics.

Curiously, the genome more closely resembles that of the human and other vertebrate genomes rather than invertebrate genomes such as other model organisms Drosophila (Arthropoda) and C. elegans (Nematoda). Nicholas Putnam, lead author of the study elaborates that this surprising result may be due to greater retention of ancestral genes in the anemones and vertebrates, whereas these tend to be lost at higher rates in Drosophila and C. elegans.

"In many ways, the ancestral genome was not so different from ours; it was intron-rich and contained nearly complete toolkits for animal biochemistry and development,which can now be recognized as pan-eumetazoan, as well as the core gene set required to execute sophisticated neural and muscular function. The ancestor had blocks of linked genes that remain together in the modern human and anemone genomes—the oldest known conserved synteny outside of prokaryotic operons. Whereas fruit flies and soil nematodes have proven to be exquisite model systems for dissecting the genetic underpinnings of metazoan development and physiology, their genomes are relatively poor models for the ancestral eumetazoan genome, having lost introns, genes, and gene linkages."-Putnam et al. 2007. Science 317: 86-94

The sea anemone genome is estimated to contain about 18,000 genes compared to a reasonable estimate for the human genome at around 20,000 genes. These 18k genes are spread over 30 chromosomes. Furthermore, over 80% of the anemone's introns are in the same place as human's!

"Only 20 percent of the ancestral eumetazoan genes seem to be unique to animals. Fifteen percent of these seem to be completely novel - we can't identify any related gene in non-animals. The other five percent were formed through substantial modifications to very ancient genes."-Study co-author Daniel Rokhsar, quoted from UC-Berkeley press release on ScienceDaily.

“Nematostella’s genome may provide more insights into the functional evolution of human genes than many far more closely related animals.”-Co-author John Finnerty, quoted in Pennisi 2007. Science 317: 27, confirming the superiority of the sea anemone to all other phyla in being able to answer "What is the meaning life?" I know there is an anemone out there with 42 chromosomes...

This is fantastic start that will undoubtedly open many interesting doors in comparative genomics. I will be anxiously awaiting more results, especially in understanding the origin of novel genes to the animal kingdom relative to other eukaryotic kingdoms (Plantae and Fungi). The next genome? After reading the latest on Zooillogix today, it is definitely got to be Buddenbrockia plumatellae. It looks like a worm, but is completely symmetrical in cross-section. In the words of Peter Holland:

"It has no mouth, no gut, no brain and no nerve cord. It doesn’t have a left or right side or a top or bottom – we can’t even tell which end is the front!" (quoted from Physorg)

This study was also published in the latest issue of Science (way to bump up the invert presence!) and answers the paradox, what the $@#! is this thing?! Analysis of 50 genes (thats 31,092 amino acid alignments) confirms that 97% of the time Buddebrockia plumatellae clusters with medusozoan cnidarians. I would say that is pretty good evidence. The authors conclude that

"This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry."

Is that funding bells I hear ringing? This is an amazing evolutionary question on how body form is controlled at the genetic level. Let me clear things up a bit. Buddebrockia is a myxozoan. A strange group of typically amoeboid parasites, with Buddenbrockia being a parasite of bryozoans (see picture below of new cnidarian exiting a bryozoan zooid). Myxozoans have strange nematocyst-looking cells called polar capsules. Some consider them reduced cnidarians, though with the discovery of the worm-like Buddenbrockia plumatellae and some Hox genes support a bilateria origin. Confused or just weirded out? Hopefully this study lays to rest of some of this conundrum. Although, it opens up infinitely more conundrums. Such as, if these are really cnidarians, albeit highly derived parasitic forms, how can there be this amazing diversity of body form from medusoid, polypoid, amoeboid, worm-like, and planular larvae all within a single phylum. I remind you that the Cnidaria are a well-supported clade!

Photo credit: Sylvie Tops

Actually, Jelly Burgers Don't Sound Too Bad

Those cnidocysts add a little tang to the tongue, kind of like a hot sauce! Jennifer at Shifting Baselines brings us the burger d'Jour, or the reality of the United States' current consumption of seafood. If things go as projected, all that will be left are Jellies! Is that so bad? The japanese eat them, but jellies aren't very nutritious. Leatherback sea turtles, a jelly specialist, need to consume a plethora of jellies to maintain expensive physiological processes like growth, metabolism and endothermy.

Another ENORMOUS problem is the use of the word jellyfish. Not only is this wrong on so many levels, it connotates a paraphyletic meaning if you will. Fish are the last common ancestors of the Amniotes (including humans), all of which contain backbones. Clearly this isn't the case. Morphological evidence suggests that jellies, though sometimes with a rigid hydrostatic system, rock-hard carbonate skeleton, sand grain and mucus tubes, or just plain ole incorporating sediment right into the body wall, do not contain contain a backbone, nor a notocord, nor pharyngeal gill slits, or dorsal-hollow nerve cord. Molecular and morphological evidence (see trees posted at Evolgen) also places the Jellies as a more or less basal group in the animal phylogeny and well separated from fish.

Next: Sea Stars aren't fish either! It is the stated mission of The Other 95% to strike from common usage the terms "Jellyfish" and "Starfish".