On 2014 Apr 28, Daniel Macqueen commented:

Firstly, congratulations to these authors for being the first to publish a salmonid genome sequence. This is a major achievement and an important landmark for salmonid biologists and fish biologists generally. I find many of the analyses in the paper to be interesting and novel.

With that said, readers of this paper should be aware that the timing of the salmonid genome duplication (i.e. ‘Ss4r’) was already demonstrated in an earlier article that (surprisingly) was not cited by Berthelot et al. (Macqueen and Johnston 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc. R. Soc. B. 281: 20132881). See Macqueen and Johnston's earlier paper here http://rspb.royalsocietypublishing.org/content/281/1778/20132881.short?rss=1

In short, Macqueen and Johnston (2014) performed a Bayesian relaxed molecular clock and phylogenetic analysis, calibrated by the fossil record, to estimate that Ss4r occurred 88-103 Mya. The Berthelot et al. estimate (90-102 Mya) was achieved using a more basic method, but nevertheless, is strikingly consistent with our earlier independent result.

I would also like to comment on some text from Berthelot et al:

“We first use the rainbow trout genome to refine the timing of the Ss4R and we dated this event around 96 Mya (±5.5 Mya), a timing in the upper range of the previous 25–100 Mya estimation^{11^.} This result is in striking contrast with the age of the Salmonidae family, which has been estimated as 50–60 Mya ^{4,16^,} suggesting that the Ss4R occurred long before the last common ancestor of extant salmonids.”

Again, Macqueen and Johnston (2014) reported this result already. From the abstract: “Our results suggest that the event [WGD] occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the [salmonid] subfamilies diverged”.

These comments were made by Dr Dan Macqueen from the Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom. Email: daniel.macqueen@abdn.ac.uk

On 2014 Apr 28, Daniel Macqueen commented:

Firstly, congratulations to these authors for being the first to publish a salmonid genome sequence. This is a major achievement and an important landmark for salmonid biologists and fish biologists generally. I find many of the analyses in the paper to be interesting and novel.

With that said, readers of this paper should be aware that the timing of the salmonid genome duplication (i.e. ‘Ss4r’) was already demonstrated in an earlier article that (surprisingly) was not cited by Berthelot et al. (Macqueen and Johnston 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc. R. Soc. B. 281: 20132881). See Macqueen and Johnston's earlier paper here http://rspb.royalsocietypublishing.org/content/281/1778/20132881.short?rss=1

In short, Macqueen and Johnston (2014) performed a Bayesian relaxed molecular clock and phylogenetic analysis, calibrated by the fossil record, to estimate that Ss4r occurred 88-103 Mya. The Berthelot et al. estimate (90-102 Mya) was achieved using a more basic method, but nevertheless, is strikingly consistent with our earlier independent result.

I would also like to comment on some text from Berthelot et al:

“We first use the rainbow trout genome to refine the timing of the Ss4R and we dated this event around 96 Mya (±5.5 Mya), a timing in the upper range of the previous 25–100 Mya estimation^{11^.} This result is in striking contrast with the age of the Salmonidae family, which has been estimated as 50–60 Mya ^{4,16^,} suggesting that the Ss4R occurred long before the last common ancestor of extant salmonids.”

Again, Macqueen and Johnston (2014) reported this result already. From the abstract: “Our results suggest that the event [WGD] occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the [salmonid] subfamilies diverged”.

These comments were made by Dr Dan Macqueen from the Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom. Email: daniel.macqueen@abdn.ac.uk