Giant squid have a giant distribution

As many as twenty one species of giant squid have been identified, but most of these were controversial. The general consensus was that there could be one with three subspecies or up to eight distinct species. Now, research shows that there is only one species with no subspecies. This is remarkable given that giant squid are found in nearly every part of the deep sea and their populations are probably large.

Winkelmann et al. (2013) sequenced the mitochondrial genome of 43 giant squid that covered individuals from all of the most widely accepted of the proposed species. They found extremely low genetic diversity and almost no genetic structure between squid from different locations. Only basking sharks, which have long generation times, small population sizes and are recovering from a recently small population size, have lower genetic diversity.

The most likely explanation for the low genetic diversity is that sometime during the last ice-age the population of giant squid declined to a very small size. Small populations are associated with low genetic diversity because random genetic drift affects gene frequency more strongly than it does in large populations. Changes in the numbers of predators or competitors may have caused the decline, but that's just speculation.

The lack of genetic structure is interesting. It suggests that giant squid are incredibly mobile. It is unlikely to be the adults that are moving long distances as other studies show that they stay in relatively contained patches of the deep sea. That argues for long distance dispersal in the eggs and larvae of the giant squid. It is common for marine species to have larvae that disperse long distances, but dispersal distance in the giant squid is extreme.

The study only looked at mitochondrial genes, which are only inherited from the mother. The vast majority of genes are in the nuclear genome and the researchers didn't publish those results in this paper. It will be interesting to see what their results are when they come to analyse them. Sometimes the information gained from looking at the nuclear genes can be at odds with that of the mitochondrial genes because of the differences in the way the genes are inherited.

Winkelmann, I., Campos, P., Strugnell, J., Cherel, Y., Smith, P., Kubodera, T., Allcock, L., Kampmann, M., Schroeder, H., Guerra, A., Norman, M., Finn, J., Ingrao, D., Clarke, M., & Gilbert, M. (2013). Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species Proceedings of the Royal Society B: Biological Sciences, 280 (1759), 20130273-20130273 DOI: 10.1098/rspb.2013.0273

Rare whale washes up in New Zealand

Ed Yong is a great science writer with a blog on Discover Magazine's website. He has an interesting post on a whale so rare that has never been seen alive. In 2010 two individuals washed up on a beach in the north of New Zealand. They were misidentified as the related Gray's beaked whale, Mesoplodon grayi, until genetic analysis of samples taken from the dead whales showed they were in fact the elusive spade-toothed whale, M. traversii. The subject of Ed's post is a recently published paper the reports on the genetic analysis and provides the first morphological description of a complete animal.

Update
The Science Now site has a story on these whales too. It makes the claim that the beached whales were found alive. I don't know which version is correct. 

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.

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".

The evolution of living fossils

The term 'living fossil' is a problematic one because its meaning is so frequently misunderstood. The greatest misunderstanding is that a living fossil species has not evolved for tens or even hundreds of millions of years (e.g. anatomically modern coelacanths are know from 409 mya). But, this is completely and utterly wrong. Living fossils are species that are related to, and superficially resemble, other species from the fossil record. But, they can be morphologically distinguished from the fossil species and have almost certainly evolved in ways that don't preserve in stone (e.g. behaviourally, physiologically and immunologically).

Three species of coelacanth. The top two are the fossil species Coelacanthus and Macropoma, while the bottom is the extant specie Latimeria. Note that they are all similar, but easily distinguished.

So, it's a little disappointing when a usually very good science news website perpetuates this misunderstanding by starting a popular science article like this: 

The morphology of coelacanths has not fundamentally changed since the Devonian age, that is, for about 400 million years. Nevertheless, these animals known as living fossils are able to genetically adapt to their environment.

There is nothing at all surprising about populations of living fossils containing enough genetic diversity to adapt to the environment. And there is simply no good reason to assume that their genetic diversity will be any different to any other extant species. 

The paper itself does not make this mistake. The interesting thing about studying the genetic diversity of coelacanths is not because they are living fossils, but because they are considered rare and endangered. A good understanding of genetic diversity within populations and an understanding of gene flow among populations can be very informative for the development of conservation management strategies. And this is the aim of the paper.

The authors obtained genetic material from 71 adult coelacanths from 6 locations across the entire known range of Latimeria chalumnae, the East African coelacanth (L. menadoensis is a second species found off Indonesia). The genetic diversity among the coelacanths was low, as would be expected from their small population sizes. The largest population of 300 - 400 individuals occurs off the Comoros Islands and all other populations appear to derive from it. The greatest genetic diversity, however, was found in populations from Tanzania.

The sites that genetic samples were collected from. The size of the circles indicates the sample size (key at bottom) and the colours indicate the genetic types found in a population (taken from the paper).

The genetic differentiation between the Comoros population and populations in other locations shows that adaptation is still occurring, but that there is unlikely to be much gene flow among populations. Interestingly, and completely unexpectedly, there appears to be two genetically distinct populations occurring at the same locations within the Comoros Islands. It's unclear what factors are driving the differentiation in the two Comoran subpopulations.

The genetic differentiation between the populations along the African coast isn't strong. This suggests that either the populations diverged relatively recently, or that they're evolving slowly. Curiously, the authors argue that their results confirm that the coelacanths are evolving slowly. But, their data can't separate these two hypotheses. Other studies show that the genes which control morphology are evolving slowly (surprise!), but other gene regions are within the evolutionary rates for vertebrates and consistent with rates in sharks, which have similar life histories. It seems more likely, therefore, that the populations have diverged relatively recently, suggesting that populations could be being recolonised from the Comoros Islands after local extinctions. 

So, coelacanths, like other living fossils, are evolving just fine. Their populations off East Africa look to have reasonably good genetic diversity for their population numbers. But, populations will probably need to be managed separately because there is little gene flow among them.

Reference:

Lampert KP, Fricke H, Hissmann K, Schauer J, Blassmann K, Ngatunga BP, & Schartl M (2012). Population divergence in East African coelacanths. Current biology, 22 (11) DOI: 10.1016/j.cub.2012.04.053

One fish, two fish, red fish, stickleback

Last week an interesting paper on evolution in sticklebacks, a widespread mostly marine fish, was published in Nature. Sticklebacks are fascinating because populations have repeatedly become established in freshwater at various times since the last ice age. Because of this they provide an amazing system in which the processes of adaptive evolution and speciation can be investigated in the wild.

The threespine stickleback, Gasterosteus aculeatus.

Evolution is often defined as the change in allele* frequencies with time. Observations of evolution in the wild, such as previous studies on sticklebacks, show that adaptation to novel environments can happen surprisingly quickly (just 13 generations in one documented case). Too rapidly, some argue, for adaptive alleles to have arisen after the novel environment is encountered. But, the adaptive alleles may already be present in the population at low frequency.

The left image shows the skeletal differences between marine and freshwater sticklebacks. On the right are preserved specimens stained red. Note the strong divergence in morphology between the marine and freshwater forms, which can arise in just 13 generations (all images David Kingsley).

If sticklebacks adapted to freshwater through the selection of alleles that arose after they encountered the new environment, then alleles within freshwater populations should be most genetically similar to the populations they diverged form. Conversely, if adaptation occurred through selection on already existing alleles, then freshwater populations should share similar alleles with each other. And the authors tested which of these possibilities was operating in sticklebacks by sequencing the entire genome of ten pairs of sticklebacks. Each pair came from the same area, but one member was the marine form while the other was the freshwater form.

They then examined the genomes for regions that were similar among the marine or among the freshwater fish. Using two different statistical approaches to determine similarities among regions they found 242 regions (0.5% of the total genome) were identified by either test and 147 (0.2% of the total genome) that were identified by both were divergent between marine and freshwater fish. That is, just by looking at those regions in a given fish you could be reasonably confident about whether it lived in marine or freshwater.

Next the authors looked at the genes contained within the regions that were divergent between marine and freshwater sticklebacks. They found that there was a significantly higher density of genes within the identified regions that the genome overall. Then, using the 64 regions that showed the strongest differentiation between marine and freshwater fish, they looked at whether the genes coded for proteins or had a regulatory function. Regulatory genes modify the function of other genes via proteins or RNA.

Regulatory genes were more common within the 64 strongly divergent regions. Just 11 regions (17%) contained coding genes, while 26 regions (41%) were regulatory. The other 27 regions (43%) contained both coding and regulatory sequences, but in these regions none of the changes to coding genes produced different proteins. This strongly suggests that these regions have a principally regulatory effect on trait expression. Thus, regulatory changes account for a much higher proportion of the differences between marine and freshwater sticklebacks.

So, this study is really cool for two reasons. It shows that rapid adaptive evolution to a novel environment can be achieved using the genetic variation present in the parent population. And it shows that the regulation of when and where coding genes are expressed largely accounts for the for the differences between marine and freshwater populations. As the authors acknowledge, the next step is to determine which traits are affected by these genetic differences between marine and freshwater populations.

*Alleles are variants of genes.

Reference (open access!):

Jones, F., Grabherr, M., Chan, Y., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M., Myers, R., Miller, C., Summers, B., Knecht, A., Brady, S., Zhang, H., Pollen, A., Howes, T., Amemiya, C., Baldwin, J., Bloom, T., Jaffe, D., Nicol, R., Wilkinson, J., Lander, E., Di Palma, F., Lindblad-Toh, K., & Kingsley, D. (2012). The genomic basis of adaptive evolution in threespine sticklebacks Nature, 484 (7392), 55-61 DOI: 10.1038/nature10944

The gorilla genome

Recently the gorilla genome was published. It showed that 30% of the genome was closer to  humans or chimpanzees that chimps and humans were to each other. The creationists were delighted, for they though they thought that the 'evolutionists' had just provided them with evidence against common descent. They were wrong...

Nobody was surprised that they were wrong; it's a habit of their's. Similarly, nobody with a good understanding of evolutionary genetics was surprised that humans had some genes in common with gorillas that they didn't share with chimps. It was, indeed, expected. But, it provides an interesting lesson for some common misunderstandings of evolution.

There is a pervasive idea that humans are the pinnacle of evolution and that chimpanzees and gorillas are 'primitive'. But, in reality, chimps and gorillas have an equally long evolutionary history and have changed just as much as humans since our lineages split from one another. And one study has shown that more genes in the chimpanzee lineage have been under selection than genes in the human lineage since the split.

Another misunderstanding is that the genetic differences observed now, must have appeared at the time the lineage split. But, the divergence of two species is not instantaneous; the genetic divisions become deeper over time. Moreover, some genetic differences may have appeared long before the split and were lost, by chance, in the populations that gave rise to one lineage, but not the other. The tree diagram for individual genes may, therefore, look very different from the phylogenetic tree. This phenomenon is know as incomplete lineage sorting (ILS). 

The important thing for evolution is that on average the human genome is more similar to the chimpanzee genome than either are to the gorilla genome. And this is the case. I suspect that many of the creationists shouting about this latest paper disproving evolution know that this is the case. But, I also think they know that it is a technical and often misunderstood part of our evolutionary knowledge and are using it to spread doubt about evolution through misinformation.

To understand ILS, you have to think not just about genes, but about the populations and species that genes occur in. When there is more than one version of a gene, each version is known as an allele. In apes (and most animals) any given individual will have two copies of a gene, which may be different alleles. But, in a population there are likely to be alleles that aren't present in every individual. Similarly, in a species all possible alleles may not be present in every population.

As populations diverge to form species, some of the alleles present in the ancestor will be lost because they won't be present in both populations. Others, however, will be retained in both descendant species. Fast-forward to another division in one of the species and the same thing can happen. By chance some of the alleles present in the common ancestor to all three species will be present in only one of the recently diverged species and in the more distantly related group. If the creationists had read more than part of one sentence of the gorilla genome paper, they would have seen this process illustrated in the very first figure.

Figure 1 from Scally et al. (2012) showing the phylogenetic tree for humans (H), chimpanzees (C), gorillas (G) and orangutans (O) with an example of incomplete lineage sorting overlaid in grey. In the example, the branching of one gene (grey line) does not map with the average genetic distance between species (percentages at the bottom). If we were to look at the example gene only, we would infer a more recent common ancestor for chimps and gorillas than for humans and chips. And that's why we don't construct phylogenetic trees based on single genes. 

Further reading:
Scally, A., et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175 


Bakewell, M. A., Shi, P., and Zhang, J. (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences 104 (18) 7489-7494