Tuesday, December 22, 2015

The Messy Science of Tardigrades

[Image source.]

Recently there has been some controversy in the news about the evolution of genomes in tardigrades. In particular, one recent paper claimed to see evidence for large-scale horizontal transfer of genes from bacteria/etc. into tardigrades, while another recent paper claimed to see no evidence for horizontal transfer.

The meat of the issue comes down to exactly how each group assembled the genomes they analyzed and published about.

Group 1:
  1. Illumina-seq (shotgun sequencing) with paired-ends.
  2. Notice lots of bacterial, etc. genes.
  3. Re-sequence genome using PacBio extremely-long-reads.
  4. Validate presence of bacterial/etc. sequences in tardigrade genome.
  5. Publish paper!
Group 2:
  1. Illumina-seq (shotgun sequencing) with paired-ends.
  2. Notice lots of bacterial/etc. sequences.
  3. Filter out bacterial/etc. sequences before constructing final genome.
  4. Publish counter-"paper"!

The first group first sequenced with paired-end reads using Illumina technology, then did re-sequencing using the extremely-long-reads of PacBio technology. This two-method sequencing allowed them to more reliably validate if the bacterial/etc. sequences were actually found contiguously in the DNA of the tardigrade or not. Any artifacts from one technique would likely not be found in the second independent technique. Any results shared between them thus have a higher confidence. The PacBio sequencing wasn't as comprehensive as the Illumina sequencing, so there wasn't complete validation of all cases of horizontal gene transfer. There is the potential that they've over-estimated the level of horizontal gene transfer. However, their methodology would allow them to see the difference between massive horiztonal gene transfer in the tardigrade's evolutionary history vs. the presence of contaminating DNA in the sample being sequenced.

The second group didn't put the same level of rigor into their sequencing. They used Illumina technology (as the first group), followed by intensive filtering of sequences which seemed to have an origin from contamination. They argue the bacterial/etc. genes seen in the first group's genome assembly were due to contamination. However, their result is exactly what would be expected from their methodology whether there was actually massive horizontal gene transfer in the tardigrade's history or not. I'm not convinced that their method would have been able to tell the difference.

A detail of the first group's results that lends credence to their interpretation over that of the second is that the bacterial/etc. genes found in the tardigrade's genome were not simply a random selection of genes as would be expected from a contamination origin. Instead, they were a selection of genes involved in DNA repair and stress response. These are exactly the sort of genes that would be expected to favor the survival of the tardigrades that had incorporated them.

Another section of the first group's results which were overlooked by the second was that the bacterial/etc. genes found in the tardigrades show evidence of having evolved inside the tardigrades for an extended period of time. The bacterial/etc. genes show a shift in the codon usage to be more like that of native tardigrade genes. As well, the bacterial/etc. genes have gained introns (something not found in bacteria). Both of these classes of changes would be very unexpected in a scenario where contamination was the source of the DNA.

The first group probably over-estimated the level of horizontal gene transfer in the tardigrade. The second group probably under-estimated the level of horizontal gene transfer in the tardigrade. So...  what is going on? This entire event shows very well how science is done in real life. Someone will have an interesting result. Someone else will produce an apparently contradictory result. Over time, the new results get closer and closer to telling us what the reality is.

The real world is messy. Science is, at its best, an attempt to understand what is happening in the world. It isn't telling people what should be, or what might be, but what actual is. The apparent uncertainty seen in regards to the tardigrades may confuse people who might be used to watching fictionalized representations of science that always seems to get everything right on the first try, or those who trust in science to get the right answer without realizing the extended process that getting the right answer can be. In the end, it is a good thing. All the interest the results in these papers has produced will likely inspire more research to be done which will add further clarity to what is going on in these interesting little creatures.