ENCODE continues to fester

Many expert bloggers are still annoyed with the science communication failure that was the ENCODE project's coverage in the popular science press. Larry Moran has another post about it regarding the profile of lead coordinator of ENCODE, Ewan Birney. And I have just run across a great collection of links to stories that more critically examine the ENCODE claims on Ryan Gregory's blog.

Vampire squid

Ed Yong is a science writer who's work I often enjoy reading. He has an interesting piece about vampire squid, Vampyroteuthis infernalis, that he has written for his blog "Not Exactly Rocket Science". Vampire squid are not actually squid, although they are related to squid and octopus. They are classified in their own order of cephalopods, the Vampyromorphida, in which they are the only known extant species.

A little fish makes big sand sculptures

In the ocean off Japan an industrious pufferfish has been crafting elaborate sand sculptures. And they're spectacular!

The sculptures created by the pufferfish (photos Yoji Ookata)

The sculptures appear to be sexually selected. Only the males make them and females prefer to mate with males who make sculptures with more ridges. During mating the eggs are laid into the center of the sculpture where they may receive some protection from the currents preventing them from being dispersed far and wide.

A male pufferfish creating a sculpture (photo Yoji Ookata)

These pufferfish (I can't work out the species) are not the only fish to make sand sculptures. Many species of African cichlids make structures, known as bowers (after the bowerbird), that function in sexual selection too. But, for many species the bowers, although they appear nest-like, do not hold the eggs. The female broods them in her mouth until they hatch and often longer.

A male cichlid patrols his volcano shaped sandcastle in Lake Malawi (photo Justin Marshall)

Unflappable albatrosses

Wandering albatrosses, Diomedea exulans, are among the largest flying birds in the world and are renowned for soaring flights of thousands of kilometers to feed. Several adaptations allow their flight to be extremely energy-efficient. For instance, their extremely long wings allow them to glide remarkably long distances and a modified tendon allows them to hold their wings open without the use of their muscles.

A wandering albatross showing its fight position (photo Wikipedia)

For a long time, it's been clear that albatrosses are using wind energy to power their flight. Indeed, Lord Rayleigh proposed that albatrosses were using wind shear to soar in 1883. Although other mechanisms have been proposed, dynamic soaring in wind shear has since been cited as the principle mechanism that they are able to gain energy from the wind. 

At the ocean surface the wind travels more slowly because of friction, but as you move away from the surface wind speeds get higher. Albatrosses can gain airspeed by rising away from the sea into the faster winds and then dropping back into the slower winds at the surface. They first turn into the wind and rise followed by a turn with the wind as they descend, gaining energy in both directions while losing some to drag.

The dynamic soaring cycle of an albatross. It starts with a turn into the wind, then a climb in altitude, then a turn with the wind and a descent back to the sea surface. The length of yellow arrows to the left of the figure indicate the strength of the wind at different altitudes (Image taken from Sachs 2005).

Penncuick argued that albatrosses couldn't get enough energy from the wind-gradient and must be deriving a large amount of energy from moving in and out of the pockets of almost still air in the lee of wave crests, which he termed 'gust soaring'. Other authors have suggested that they slope-soar off the windward side of wave crests. But, the debate over how albatrosses are gaining enough energy for their long distance flights has played out in the theoretical literature, sometimes accompanied by anecdotal observations of flight behaviour.

The gust soaring cycle of an albatross. As the albatross moves through the 'separated boundary layer' (blue line) from the leeward side of a wave crest it gets a kick of energy from the wind allowing it to gain altitude and potential energy to power its soaring flight (Image taken from Richardson 2011)

With their paper published recently in PLOS One, Sachs et al. have added some empirical data to help resolve the issue. They attached small GPS devices to the backs of 16 albatrosses, which measured the position and altitude of each individual once every second and the velocity 10 times a second. This allowed them to look at the small scale of the flight cycle and draw inferences about the physics of the manoeuver.

A plot of a recorded dynamic soaring cycle. The numbers indicate each stages from the ascent [1], to the turn at peak altitude [2], to the descent [3] and the turn to restart the cycle [4] (Image taken from Sachs et al. 2012).

They used the data to calculate the total energy over the entire dynamic soaring cycle by summing the potential and kinetic energy. Contrary to the expectations of gust soaring and slope soaring, the maximum energy in the cycle was reached on the descent. And the energy accumulation was gradual, without any large spikes that would result from a big kick in energy close to the surface.

A two-dimensional plot of the soaring cycle showing the point at which maximum and minimum energy are reached. The track shown here is the same as the one above (Image taken from Sachs et al. 2012).

Sachs et al. also calculated the energy gain that the albatrosses could achieve throughout the cycle. The maximum energy in the cycle was ~360% of the minimum energy and provided enough surplus to overcome drag forces. Indeed, the energy gain was so large that it far exceeded what the albatrosses could achieve by flapping their wings.

The efficiency that the albatrosses converted the wind into usable energy for flight allowed them to achieve ground speeds higher than the wind speed. On average the 16 birds that they followed traveled at ~60 kilometers per hour, but one bird was clocked traveling at an average of 76 kilometers per hour. If that's not amazing enough, an earlier study that Sachs et al. cite, clocked a grey-headed albatross (Thalassarche chrysostoma) traveling at an average ground speed of 110 kilometers per hour for 9 hours in high winds! 

My only concern about the paper, which isn't a very big one, is that all of the energy calculations are based on a single dynamic soaring cycle (the one in the two figures above). The authors do present three others in their supplementary material, which all look essentially the same. But, I wonder why they don't use them for the calculations. And they tracked 16 birds for at least 176 kilometers, did they really only get four cycles which occur in the space of ~150 meters? They don't say.

References:

Sachs G, Traugott J, Nesterova AP, Dell'omo G, Kümmeth F, Heidrich W, Vyssotski AL, & Bonadonna F (2012). Flying at no mechanical energy cost: disclosing the secret of wandering albatrosses. PloS one, 7 (9) PMID: 22957014  

Richardson PL (2011). How do albatrosses fly around the world without flapping their wings? Progress in Oceanography, 88 (1 - 4), 46-58 DOI: 10.1016/j.pocean.2010.08.001  

Pennycuick CJ (2002). Gust soaring as a basis for the flight of petrels and albatrosses (Procellariiformes) Avian Science, 2 (1), 1-12

Top five on Friday

On his website "Why Evolution is True", Jerry Coyne has posted pictures of a pretty spectacular looking snail, Blaesospira echinus. So, I thought that today I would post my top five favourite mollusks. There were two mollusks in last week's list of my top five favourite marine animals. To give the other amazing species in phylum Mollusca a chance, I'll leave them out.

1. Elysia chlorotica

It was hard to keep this one out of last week's list. Like Glaucus atlanticus (who was number 1 last week), it steals cells from the organisms it eats and uses them for its own ends. In Elysia's case, it steals chloroplasts from the seaweed Vaucheria litorea. It's able to keep these alive for up to 9 or 10 months, which indicates that it has acquired genes for this task, probably by horizontal gene transfer.

The beautiful and fascinating Elysia chlorotica (Photo Wikipedia)

2. Giant squid, Archieteuthis dux

It's the second biggest invertebrate, after the colossal squid. And like the colossal squid, it has the biggest eyes of any animal. Eight species of giant squid have been named, but it's almost certain that there are fewer species and there may be only one, A. dux. 

The first live giant squid ever to be photographed in its natural habitat, the deep sea (photo Kubodera and Mori)

3. Dorytethis opalescens (formerly Loligo opalescens)

Like most cephalopod mollusks, D. opalescens is an amazing colour changer. But, unlike many other cephalopods it uses two different cell types to change colour (see here for an amazing bit of science communication explaining it all). It lives close to the surface and one of the reasons for its colour changing skill is thought to be that it avoids predators by countershading the light-dark patterns of wave lensing.

Doryteuthis opalescens (photo Wikipedia)

Wave lensing pattern on a sandy seafloor (Photo National Geographic)

4. Giant clam, Tridacna gigas

It's big, it's beautiful. Like corals, all of its colouration comes from symbiotic algae living inside its body.

The giant clam, Tridacna gigas (photo Wikipedia)

5. Janthina janthina

A bubble rafting snail that lives in the open ocean. The bubble raft is likely to have evolved from an ancestral egg coat.

The bubble rafting snail Janthina janthina (photo Denis Riek)

ENCODE: Great science, poor communication

Last week the ENCODE project published 30 papers in three different journals, Nature, Genome Research and Genome Biology. In the summary paper, they claimed that they had found a function for 80% of the genes in the genome. However, in order to make this claim it seems they have had to redefine 'function' to have a meaning that most people wouldn't accept as meaningful.

We know that only about 1 to 1.5% is used to make proteins and the ENCODE project's findings didn't change that figure. A lot of DNA is transcribed into RNA and some of that RNA has a regulatory role, that is it regulates gene function by turning them on and off. ENCODE found that adding the amount regulatory DNA to protein ecoding DNA and you get to a figure of 9%. This is higher than was expected and is an exciting result.

Getting from 9% to 20% was all estimation. The ENCODE project looked at 147 different human cell types, but there are at least 210 and possibly many more distinct human cell types. Based on their incomplete coverage of cell types, ENCODE researchers believe that there is at least another 11% of the genome that is regulatory. But, this remains to be demonstrated.

The final 60% is part DNA that's meant to help package the DNA helix, part that has sites that proteins bind to and part DNA that's transcribed into essentially meaningless RNA (I might have missed some things here). The argument for including this 60% in the estimate of how much of the genome is 'functional' seems to boil down to the idea that is does something and evolution wouldn't let it do something if it wasn't useful. Other than this, there seems little merit in including this 60% as functional.

If my suspicions about the argument are correct, it's adaptationist nonsense. The amount of non-coding DNA, also called 'junk DNA', is variable among species. For instance, the genome of the pufferfish, Takifugu rubripes, is ~365 million base pairs, while genome of the lungfish, Protopterus aethiopicus, is orders of magnitude larger at ~133 billion base pairs. Much of the lungfish genome would be functional under the ENCODE definition, but if it's important, how come the pufferfish can get away with 0.3% of the base pairs*?

The media coverage of the ENCODE publications has focused on the 80% figure, without much discussion of what is meant by 'functional'. This is unfortunate because the definition of 'functional' is critical for evaluating the findings. In my opinion, 80% is a fudge that can only be reached by a weaseling use of language. It's clear to me, from the variation in genome size among species and that we can remove large sections of non-coding DNA with no observable effect, that most of our genome has no important function. The ENCODE project has not shown it to be otherwise.

Other coverage that I thought was good:

T. Ryan Gregory - A slightly different response to today's ENCODE hype

Michael Eisen - A neutral theory of molecular function

Sean Eddy - ENCODE says what?

Brendan Maher - Fighting about ENCODE and junk

John Farell - Reports of junk DNA's demise have been greatly exaggerated


* This is Ryan Gregory's "Onion Test".

Top five on Friday

Over at Deep Sea News they've been composing bucket lists of marine species (here and here). So, today I thought I would compose a top five list of my favourite marine species.

1. Glaucus atlanticus

It steals the stinging cells from its cnidarian prey and uses them for its own protection. Amazing!

The beautiful and amazing Glaucus atlanticus (photo Wikipedia).

2. Colossal squid, Mesonychoteuthis hamiltoni

The biggest invertebrate known by weight. The giant squid, Architeuthis dux, may grow to be longer, but only because of its long feeding arms. Without the arms, the colossal squid is longer.

At 495 kg, this is the biggest colossal squid that has been caught. We know from beaks recovered from the stomachs of sperm whales that there are much bigger ones out there (photo Wikipedia)

3. Flying fish, Cheilopogon pinnatibarbatus

There are a large number of flying fish in the family Exocoetidae, I like them all. I chose C. pinnatibarbatus because it is found off the Australian coast.

The Atlantic flying fish Cheilopogon malanurus, which looks similar to C. pinnatibarbatus (photo Wikipedia)

4. Antarctic krill, Euphausia superba
What they lack in size, they more than make up for in number. With an estimated biomass of 500 million tonnes, they are probably have a greater total mass than any other species.

Euphausia superba (photo Wikipedia)

5. Blue whale, Balaenoptera musculus
The biggest animal to have ever lived. What other reason do you need?

Balaenoptera musculus, the biggest animal ever (photo Wikipedia)

Rapid speciation in starfish

Australian waters are extremely rich in starfish species. Indeed, a little over 15% of all known species of starfish occur in Australia. For at least two of these starfish, speciation occurred extraordinarily fast. At most, they became separated about 22 thousand years ago, but the best estimate for the timing of the split is about 6 thousand years ago.

We know that evolution can be very rapid (e.g. sticklebacks) and that sometimes this leads to speciation (e.g. cichlids). But, in these cases selection is probably acting on a small number of alleles that are already present in the population. What makes the starfish study so breathtaking is that there has been profound changes to life history in the two species, which likely involved selection on many morphological and physiological traits.

Puritz et al. looked at Cryptasterina pentagona and its sister species C. hystria. Like most starfish, C. pentagona has separate sexes and reproduces by 'broadcasting' sperm and eggs into the water column where fertilisation occurs. In stark contrast, C. hystria produces both sperm and eggs simultaneously, and it exclusively self-fertilises within its own body cavity. The embryos of C. pentagona develop in the plankton, while C. hystria broods its offspring within the gonad until they are ready to emerge as small starfish.

It takes an expert to distinguish Cryptasterina hystria (top) and C. pentagona (bottom) in the wild. In fact I've seen the bottom picture shown as C. hystria and C. pentagona, but I think I got it right (photo Jon Puritz).

Puritz et al. speculate that water temperature may have provided the selective pressure that favoured the evolution of the C. hystria life history. Viviparity, like that seen in C. hystria, has been documented in a number of other starfish species. And it is consistently associated with species that occur in colder water. The two Cryptasterina species are separated by about 375 kilometers, with C. pentagona in the warmer north and C. hystria to the cooler south.

The authors also argue that small population size may have selected for self-fertilisation. If there are so few individuals in the population that your gametes are unlikely to meet another individual's, it's better to fertilise your own than to not reproduce at all. It's expected that genetic variation in a population that self-fertilises should be very low. But, genetic variation in C. hystria is so low it suggests the whole species derived from very few individuals, perhaps just a single one.


The transition from broadcast spawning with planktonic larval development to self-fertilisation with larvae brooded within the gonad has occurred in another Cryptasterina species, C. pacifica. In the closely related genus Parvulastra, a similar transition has occurred too, but probably over 500 thousand years. This suggests that the genetic variation required for the dramatic shift in life history is widely present in the group of starfish to which the genera Cryptasterina and Parvulastra belong. But, the speed at which evolution has occurred is truly astonishing.

Parvulastra exigua, note its similarity to the Cryptasterina species (photo Museum Victoria).

Puritz JB, Keever CC, Addison JA, Byrne M, Hart MW, Grosberg RK, & Toonen RJ (2012). Extraordinarily rapid life-history divergence between Cryptasterina sea star species. Proceedings. Biological sciences / The Royal Society, 279 (1744), 3914-3922 PMID: 22810427

Hermit crab migration

On Tuesday I wrote about a crustacean with an unusual larval form. The larvae occur in mid-water while the adults occur in the deep sea. Habitat shifts associated with changes in life history stage are not uncommon and some of them are even more dramatic than changing depth. Take the hermit crabs in the Virgin Islands. The adults are terrestrial, but the larvae develop in the sea. The adults must migrate to the waters edge in order to reproduce and release their eggs into the water.

Hermit Crab Migration from Steve Simonsen on Vimeo.

Hermit crabs are not true crabs. True crabs are in the crustacean infraorder Brachyura, while hermit crabs are in the infraorder Anomura. There are Brachyurans that perform similar mass migrations to release their eggs into the sea. One of the best known is the migration of the Christmas Island crab.

If the eggs and larvae survive out in the ocean, tiny juveniles climb back onto land and migrate into the forests where they grow into adults. In most years, only a very small number will make it back to land. In some rare years, the numbers that arrive on the shore are mind-boggling.

Carnival of Evolution #51

The Carnival of Evolution number 51 is up at 'The Stochastic Scientist'. My post on beak size in birds made the list.

An unusual crustacean meets its parents

Many animals living in the ocean have complex life histories where the young look nothing like the adults and often occupy different habitats. Frogs, with their early tadpole stage, are classic examples of animals with complex life histories. But, tadpoles look far more like frogs than the larvae of other animals resemble their adult forms. Different species of distantly related crustacean larvae, for instance, can look far more like each other than they resemble the adults of their own species.

The nuaplius larvae stage (left) of a cylopoid copepod (top) and penaeid shrimp (bottom) and their adult forms (right). These distantly related crustaceans appear similar as larvae, but not as adults (images Wikipedia)

Because larvae look so different from the adult form, identifying the species that larvae belong to can be tricky. Often it requires the larvae to be carefully reared in the laboratory to see what they eventually turn into, but this isn't always possible. In some cases, it is possible to place larvae within a species using genetic techniques, but this requires a DNA sequence from the adult to compare to.

One type of crustacean larva that has been difficult to assign to an adult form are the Cerataspids. There are three known species that have been placed in two genera, Cerataspis monstrosa, C. petiti and Cerataspides longiremus. Like many unusual crustacean larvae, the first to be discovered (C. monstrosa in 1828) was thought to be an adult of the crustacean order Leptostraca. However, it later became apparent that they were probably larvae of shrimp within the Penaeoid superfamily, possibly from the family Aristeidae.

The crustacean larva Cerataspis monstrosa (image from Bracken-Grissom et al. 2012)

Through a combination of skill and luck, Bracken-Grissom et al. were able to resolve the adult identity of C. monstrosa. The luck involved getting their hands on a specimen of the larva that was suitable for DNA analysis. Almost all we know about C. monstrosa comes from examining specimens in the gut contents of its predators, like skipjack tuna. But, Bracken-Grissom et al. unexpectedly obtained a single specimen from a trawl at a depth of 420 meters in the Gulf of Mexico.

Bracken-Grissom et al. collected DNA sequence data from the specimen and compared it to sequences of crustaceans available from a database of genetic sequences. Because C. monstrosa had been liked with Penaeoid shrimp in the family Aristeidae, they concentrated their analysis within those taxonomic groups. And they hit pay dirt. The DNA from the C. monstrosa specimen was a near perfect match with a deep-sea Aristeid shrimp Plesiopenaeus armatus.

The Aristeid shrimp Plesiopenaeus armatus (image from Bracken-Grissom et al. 2012)

Plesiopenaeus armatus has a similar geographic distribution to C. monstrosa, but it is known from deeper water. The contrast between the larval habitat and  adult habitat is not unusual for organisms with complex life histories. Indeed, many complex life histories involve much more dramatic habitat shifts. However, the transition from mid-water pelagic larvae to abyssal adults is not known in many species.

The findings of Bracken-Grissom et al. have implications for the other species of Cerataspis larvae that haven't been linked to their adult form. They suggest that C. petiti is the larva of the only other known species in the genus Plesiopenaeus, P. coruscans. Further they suggest that Cerataspides longiremus is the laval stage of a closely related Aristeid shrimp, possibly an unidentified representative of the same genus.

Bracken-Grissom HD, Felder DL, Vollmer NL, Martin JW, & Crandall KA (2012). Phylogenetics links monster larva to deep-sea shrimp Ecology and Evolution DOI: 10.1002/ece3.347