Creationists blow a fuse over chromosome 2

A while ago the gorilla genome was published. And it was pointed to by creationists as evidence that evolution is wrong (see my post here). Now the gorilla genome is fueling another spat between the forces of creationism and science. In particular what information that the gorilla genome can provide to help sort out the fusion on human chromosome 2.

Carl Zimmer explains the new evidence for fusion on his blog "The Loom". The discussion of the evidence for chromosome fusion is a prelude to a great story about creationist posturing and misdirection. Carl simply wanted to know what evidence there was to support their claim that the fusion of chromosome 2 couldn't have occurred since the split of our lineage from the chimpanzee lineage.

To hide the fact that there is no evidence to support this claim, they challenged him to a debate. When he turned them down for various good reasons and restated that he just wanted some evidence to support their claim, they crowed that he had folded. But, Larry Moran points out that they only like debates when they are on their turf and on their terms. Let's not forget that he didn't fold, he is still asking for evidence.

Let's also not forget that Carl has already outlined the case he would espouse in the debate. The creationists have not responded to the claims Carl made in his original post in any meaningful way. The fury with which they have confronted him is, to me, a little surprising. But, Larry Moran calls it "typical" and speculates about why Carl's request for evidence might have caused so much fuss.

***Update***

The creationists have now provided Carl with the evidence he was requesting. And, as expected, it's completely pathetic. Basically the evidence boils down to misrepresenting the findings of a paper that has been superseded by the more recent findings that Carl describes in his original post. On the upside, I've learnt some interesting things about chromosomes and genome evolution that I probably wouldn't have otherwise.

Two's company, three's community ecology

A few days ago I wrote about a review paper in Nature Geoscience, which concluded that seagrass meadows were better at storing carbon than terrestrial forests. One of the reasons for this is that, rather than being broken down to carbon dioxide, the organic matter beneath seagrass meadows is broken down anaerobically to hydrogen sulphide.

Hydrogen sulphide is toxic to the seagrass and should build up as more organic matter accumulates over time. Until a new paper in Science, it was unclear how the plants coped with the gas. Seagrasses do transport oxygen to their roots, which is released into the surrounding soil, mitigating against the toxic effects of sulfide. But, sulfide production can outpace the transport of oxygen, especially at higher temperatures, which should result in reduced productivity and mortality. 

Seagrass meadows are, in contrast, persistent and highly productive, which suggests that there's more than oxygen transport going on. The paper provides data to show that burrowing Lucinid bivalves commonly co-occur in high abundance with seagrass meadows. And furthermore, the Lucinids increasingly diversified as seagrasses evolved and became more common in the oceans.

A map showing the locations where seagrass occur with (green spots) or without (red spots) lucinid bivalves. The bivalves were present in 97% of tropical, 90% of subtropical, and 56% of temperate seagrass meadows (image taken from the paper).

Lucinids are known to form symbiotic relationships with sulfur oxidising bacteria. The bivalves bring oxygen and sulfides to their gills where the bacteria use them to fuel the production of sugars, which feed them and their bivalve hosts. The paper hypothesises that seagrass also participates in the symbiosis through the transport of oxygen to its roots, which provides ideal conditions for the lucinids and their gill bacteria.

The lucinid bivalve Loripes lacetus (photo idscaro seashell directory)

They tested the hypothesis by growing both a lucinid bivalve (Loripes lacteus) and a seagrass (Zostera noltii) in the laboratory. They examined the effect of sulfide on the bivalve and seagrass when they were both present or when the partner was absent. And their results were intriguing, particularly the effects on seagrass.

The seagrass Zostera marina, which is very similar to Z. noltii (image wikipedia)

The seagrass had greater biomass of both leaves and roots when no sulfide was added and the bivalves had higher weights relative to their shell size when it was. But, when sulfide was added both the seagrass and the bivalve did better when they both occurred together. Interestingly, the seagrass did best when the bivalve was present, but no sulfide was added. This seems to be because sulfide built up in the treatments, even when it was not added.

The results largely confirmed the hypothesis that there is a three species symbiotic relationship. Seagrass benefits from the removal of sulfide by the bacteria-bivalve symbiosis and the bivalve benefits from the oxygen provided by the seagrass. Furthermore, in the wild the bivalve may benefit from the presence of seagrass because seagrasses indirectly stimulate sulfide production by accumulating organic matter in the soils beneath the growing meadows.

The results have potentially significant implications for seagrass conservation. Many conservation projects attempt to restore lost seagrass meadows by moving plants from other locations were they're doing well. But, the results of this procedure are mixed. This research suggests that moving the bivalve as well as the seagrasses might lead to greater success.

Tjisse van der Heide, Laura L. Govers, Jimmy de Fouw, Han Olff, Matthijs van der Geest, Marieke M. van Katwijk, Theunis Piersma, Johan van de Koppe, Brian R. Silliman, Alfons J. P. Smolders, & Jan A. van Gils (2012). A three-stage symbiosis forms the foundation of seagrass ecosystems Science, 336 (6087), 1432-1434 DOI: 10.1126/science.1219973

Seagrass meadows, better than forests

I've written before about how amazing seagrass is (part I and part II). A recent paper in Nature Geoscience reviews the published literature on the carbon storage capacity of seagrass meadows. And what it concludes is quite surprising. Per hectare they are better at storing carbon than terrestrial forests despite the insignificant amount of carbon in the plants themselves.

Over time seagrass meadows accumulate large amounts of organic material in soils beneath the growing plants. Part of the soil is formed by dead seagrass, but typically half of the organic material is from other sources that collect in the meadows. The amount of soil that accumulates can be substantial, sometimes forming a layer several meters thick.

The paper looked at published and unpublished data on the organic carbon content of the soils beneath seagrass meadows. They found that the seagrass soils stored almost twice as much carbon as terrestrial soils. Principally this is because the break down of organic matter in seagrass soils occurs anaerobically, which releases hydrogen sulphide, rather than carbon dioxide released in the aerobic break down occuring in terrestrial soils.

Another impressive finding of the review is that carbon stored in the seagrass soils can be stable over thousands of years. This is far longer than carbon can be stored in terrestrial systems, where fires and decomposition eventually liberate the stored carbon back to the atmosphere. However, over the last century nearly 30% of of seagrass meadows have disappeared, most likely causing the release of the sequestered carbon.

Protection and restoration of terrestrial forests is often advocated as a tool for mitigating the effects of climate change. The conclusions of the review paper suggest that restoration and greater protection of seagrass meadows might also be an important tool for reducing the amount of carbon dioxide in the oceans and atmosphere. Intriguingly, deforestation is a threat to seagrass meadows.

Seagrass meadows are exposed to a number of anthropogenic threats. Poor land-use practices, such as deforestation, that increase the silt and nutrient loads that reach seagrass meadows are the most common cause of meadow degradation and loss. Increased turbidity, caused by both silt and nutrient loads, reduces the amount of light penetrating to seagrass meadows. In addition, high nutrient loads can cause the increased growth of epiphytic organisms.

The capacity of marine ecosystems to help mitigate against the effects of climate change is increasingly being looked at. And they are showing that they are not only important pieces in the puzzle, but that they could be more important than terrestrial systems.

James W. Fourqurean, Carlos M. Duarte, Hilary Kennedy, Núria Marbà, Marianne Holmer, Miguel Angel Mateo, Eugenia T. Apostolaki, Gary A. Kendrick, Dorte Krause-Jensen, Karen J. McGlathery & Oscar Serrano (2012). Seagrass ecosystems as a globally significant carbon stock Nature Geoscience, 5 (7), 505-509 DOI: 10.1038/ngeo1477

Arsenic life not based on arsenic...

Few people who read popular science websites would be unaware that about this time last year a paper was published in Science that claimed a bacteria could incorporate arsenic into its DNA. The paper sparked a storm of controversy for the way the news was announced at a press conference and for the way that the science was done. The lead author, Felisa Wolfe-Simon, NASA (who funded the research) and even Science took flak for the publication of the paper (see Carl Zimmer's compendium of critical responses).

Now one of the most vociferous critics, Rosie Redfield, has published a paper with a team of other researchers that has failed to replicate the results of the initial paper. Another team has also published a paper alongside the Redfield paper. They too, failed to reach the same results as Wolfe-Simon. The conclusions of both the new papers were essentially the same; there was enough phosphorous in the medium to allow the bacteria to grow and there was not arsenic in its DNA.

But, it is apparently not the end of the saga. Felisa Wolfe-Simon has stated that the two new papers "are consistent with our original paper". The new results are completely at odds with the claims made in the initial paper, so it'll be interesting to see how she demonstrates that there are no discrepancies. She has promised that she and her collaborators will have a new paper out in the next few months.

New feathered dinosaur

I've said in the past that the lion's share of the really amazing fossils, in terms of preservation and importance, seem to be coming out of China in the last 10 years or so. But, now an exceptionally well preserved theropod dinosaur has been unearthed in Germany. And it's important too. It's a feathered theropod dinosaur that is only distantly related to the group of theropods that gave rise to the birds.

A photograph of the new feathered dinosaur fossil, Sciurumimus albersdoerferi. The scale bar shows 5 cm, so, as it's name suggests, it's about the size of a squirrel (image taken from the paper).

The researchers gave it the name Sciurumimus albersdoerferi. The genus name means squirrel mimic because the feathers on its tail make it bushy like a squirrel's. The species name is given in honour of Raimund Albersdörfer, who made the specimen available to the researchers for their study.

The fossil is important for a couple of reasons. The first is that it is distantly related to other theropod dinosaurs that we know for sure had feathers. Which pushes the evolution of feathers back closer to the common ancestor of all theropods. Combine this with the evidence that some heterodontosaurs had feathers and the hypothesis that the common ancestor of all dinosaurs was feathered gains some weight. But, the independent evolution of feathers in the theropods and heterodontosaurs is far from refuted.

A phylogenetic tree of theropod dinosaurs. We know feathers are present in group 4 (at the bottom) and now group 8 (in the middle), which takes the evolution of feathers back to at least group 2. This group, known as the Tetanurae ("stiff tails"), includes most theropods (tree taken from the paper).

The other reason this fossil is important is that it is the best preserved fossil megalosauroid thus far discovered. Indeed, it provides the only complete megalosauroid skeleton. Therefore it provides evidence that helps resolve several questions about the evolution of traits in theropods, such as the evolution of bones in the hand.

An interesting side note is that this fossil is of a very young individual, which probably died soon after hatching. Therefore, the bushy tail is almost certainly not a sexually selected character. This pours some cold water on the hypothesis that feathers evolved in dinosaurs primarily as a means to signal mate quality, which was claimed in another recent paper.

Rauhut, O. W. M., Foth, C., Tischlinger, H., & Norell, M. A. (2012). Exceptionally preserved juvenile megalosauroid theropod dinosaur with filamentous integument from the Late Jurassic of Germany Proceedings of the National Academy of Sciences, (Early Edition) DOI: 10.1073/pnas.1203238109

Marine parks and the Great Barrier Reef World Heritage Area

One of the biggest stories in marine conservation in Australia this year is the announcement that 2.3 million square kilometers of Australian waters will receive some form of protection in marine reserves. About a third, or 800 thousand square kilometers will be fully protected as Marine National Parks. This new announcement takes the total area protected by the Federal Government to 3.1 million square kilometers. Which is all cause for some optimism.

A map of the newly declared marine reserve network in Australia. Green denotes the areas which are fully protected as Marine National Parks. Yellow denotes 'special protection areas' which exclude commercial fishing, but allow recreational fishing. Dark blue denotes 'special purpose zones', which allow only some forms of commercial fishing. Light blue denotes 'multiple use zones', which only prevent the most destructive commercial fishing practices. The grey areas in the south-east are the bits of the reserve network that were established in 2007. If you would like a PDF of the map, and other information go here.

The largest contiguous protected area is the Coral Sea Marine Reserve, which adds to the already established Great Barrier Reef Marine Park. There was a storm of criticism when the Coral Sea Marine Reserve draft plan was released because many experts believed that it did not go far enough to protect the reef. In a rare win for the environment, the Australian Government extended the boundaries in the final plan.

A map of the Coral Sea Marine Reserve. Colours denote the same levels of protection as above. If you would like a PDF of the map, and other information go here.

There is, however, still significant disquiet about the future of the Great Barrier Reef, which is estimated to have lost half of its coral cover in the last 50 years. A UNESCO mission to Australian in March strongly criticised the management of the reef and indicated that its listing as a World Heritage Area was at risk of being downgraded. Several of the threats that UNESCO identified will not be addressed by the new marine reserves. 

The UNESCO mission identified climate change, catchment runoff, coastal development, ports and shipping, and fishing as the most pressing threats to the Great Barrier Reef World Heritage Area. Three of these (catchment runoff, coastal development and climate change), are due to activities outside the marine reserve and World Heritage Area. Moreover, the other activities will be allowed in at least some areas of the new marine reserve. 

The cynic in me can't help also noticing two things. Firstly, that the bulk of the areas that receive full protection as marine national parks are generally those which are furthest offshore, where impacts are already low. And, secondly, that there will need to be enforcement of the new restrictions, but there is mention of additional funds to achieve this. Apparently, enforcing compliance will be achieved using existing infrastructure; infrastructure that is already used for other important activities.

Despite my slight cynicism, I think the new marine reserve network is excellent news for the conservation of the marine environment in Australia. But, the network doesn't address all of the threats to Australia's seas. And there are at least three state governments (Victoria, Queensland and Western Australia) that have ignored environmental threats and sought to erode existing protections. It would be incredibly embarrassing for Australia on the world stage and disastrous for Queensland's marine tourism industry if UNESCO were to downgrade the Great Barrier Reef World Heritage Area listing.

Further reading

For the UNESCO mission report go here.

For the Great Barrier Reef Outlook Report, which sparked the UNESCO mission, go here.

For an interesting expert commentary on the UNESCO report go here.

UPDATE:
Just after posting this article I found another article that is more hopeful that the protections granted by the new marine reserves will be adequately enforced. I think they can be too, but enforcement needs funding and I haven't seen those details yet.

Flatfish eyes: The twice solved mystery

You know it's particularly mysterious when a puzzle stumps Charles Darwin and all the egghead evolutionary biologists that have come since. But, how both eyes of flatfish came to be on the same side of the head was such a bafflingly mysterious puzzle that it needed to be solved twice. By the same person.

The turbot, Psetta maxima (image Wikipedia)

In 2008, Matt Friedman was able to show that the transition to both eyes on the same side of the head was gradual. Now, in 2012, Matt Friedman has done it again and solved the mystery of the flatfish head by demonstrating that the transition to both eyes on the same side of the head was gradual. Or perhaps, in both instances the journalists overcooked the story and tried to make an interesting incremental step in our understanding of the evolution head asymmetry in flatfish into a revolution in understanding.

But, behind every popular science article beat-up of stumped boffins and puzzling riddles, there's usually some interesting science. And that's the case here. 

Flatfish are fascinating creatures. Adults live on the bottom, lying on one side, with both eyes gazing up from the same side of their head. At hatching, though, their larvae look unremarkable in comparison to other fish larvae. Their eyes are on opposite sides of their head and they swim vertically. But, late in their larval development one eye begins to migrate upwards and over the top of the head until it sits near the other eye.

Larval stages of the summer flounder Paralichthys dentatus. Each letter denotes a stage in development and 'early' and 'late' indicate the position withing the stage. The migrating eye is in grey. The migration begins during stage F, with the eye crossing the midline in stage H (image from Martinez & Bolker 2003).

Far from being stumped, several scientists put forward their explanations, including Darwin. Saltationists, such as Goldschmidt, saw it as evidence that some speciation events were the result of large mutations that revolutionised morphology. While others thought that the eye must have gradually migrated, as it does at the end of the larval period.

The evidence seems to have been more strongly in the gradualist camp. And not only because the new synthesis largely killed off the idea of saltation in evolution. It was already known that the more ancestral flatfish groups, such as spiny turbot and flounder, were less asymmetrical and less strongly associated with the bottom than the more derived groups, such as sole. The only thing that was lacking was truly smoking gun evidence.

Three species of flatfish. From top to bottom,  the spiny turbot, Psettodes belcheri, the flounder, Citharus linguatula, and the sole, Achirus klunzingeri. As you move top to bottom, the wandering eye moves further down the head (Pictures from FAO, via FishBase).

Enter Matt Friedman. He found several examples of fossilised flatfish species from two genra that were about 50 million years old. One genus, Amphistium, had been previously described, but had not been placed within the flatfish group. The other genus, Heteronectes, was previously undescribed. They were in the collections of European museums that, like most museums, had a heap of fossils that nobody had really looked at before. 

The two sides of the fossil fish Heteronectes chaneti. Note the eye on the left side (right hand image) is higher than the eye on the right (from Friedman 2012).

The reason that Amphistium had not been placed within the flatfish was that, although the eyes were not in symmetrical positions, the asymmetry was put down to distortion during fosilisation. Friedman was able to show in his 2008 Nature paper that the eye asymmetry was not as a result of distortion that that, therefore, Amphistium and Heteronectes were transitional between the symetrical ancestors and modern flatfish. 

A simplified phylogeny of flatfish showing the progression of eye migration over history. Next to each fish is a diagram of their skull from the left (top), top (middle) and right (bottom). The two rightmost fish are the modern genera Psettodes and Citharus, examples of which are shown above (image modified from Friedman 2008).

Interestingly, Amphistium and Heteronectes were alive at them same time as flatfish with the modern asymmetrical morphology. Which indicates that they aren't the direct ancestors of the modern flatfish and that the origins of flatfish are much older. This, in turn, suggests that the transitional morphology provided some advantages, since it persisted for so long in the presence of more modern eye arrangements.

The fossil flatfish Eobothus that was alive at about the same time as Amphistium and Heteronectes, but, like modern flatfish, had both eyes on the same side of its head (image the Fossil Forum).

How Heteronectes and Amphistium were so successful with one eye pointing at the bottom is not clear. However, extant species provide some clues. The less asymmetrical species spend more time hunting prey away from the bottom, where a downward pointing eye would be more useful. In addition, Friedman speculates in his 2008 paper that like many modern flatfish, Heteronectes and Amphistium may have used their dorsal an anal fins to lift their downwards facing eye into a position where it could be used. But, of course, all this assumes that lying on one side came before eye migration, which is not clear.

The European plaice, Pleuronectes platessa, using its dorsal and anal fins to lift itself off the bottom (image EOL).

Friedman's 2012 paper in the Journal of Vertebrate Paleontology, provides a much more detailed description of the morphology of Heteronectes. Because Heteronectes represents a transitional form, it may also share more characters with the common ancestor. The aim of the paper was, therefore, to use the described characters of Heteronectes to clarify the relationships between the flatfish and other groups of fish.

The analysis suggested that the Latids are the most closely related family of fish. But, Friedman cautions that his analysis was necessarily coarse. Some of the characters identified as uniquely shared by the Latids and Heteronectes may actually be general to a larger group of fish. And, because Friedman didn't examine other flatfish in the study (he must have another paper in the works), the characters identified in Heteronectes may not be shared with other flatfish.


So, two interesting papers. But, although we now know that evolution of the asymmetrical flatfish eye was gradual and, therefore, that transitional flatfish morphologies clearly were not useless, a lot of questions remain. For instance, we can only speculate about the selective pressures that drove eye migration and we don't yet know what the flatfish common ancestor looked like. 


References

Friedman, M. (2008). The evolutionary origin of flatfish asymmetry Nature, 454 (7201), 209-212 DOI: 10.1038/nature07108

Friedman, M. (2012). Osteology of †Heteronectes chaneti (Acanthomorpha, Pleuronectiformes), an Eocene stem flatfish, with a discussion of flatfish sister-group relationships The Journal of Vetebrate Paleontology, 32 (4), 735-756 DOI: 10.1080/02724634.2012.661352

Martinez, G. M. and Bolker, J. A. (2003). Embryonic and Larval Staging of Summer Flounder (Paralichthys dentatus) Journal of Morphology, 255, 162-176