Figure 5

[evogytis]

Figure 5: If I understand this figure correctly, the authors are using the BEAST MCC tree of each segment, looking at a particular point in the past, and counting the number of extant lineages that would be associated either with the original 1983 Yamagata virus or the original 1983 Victoria virus. I understand what the `recent past' part of this chart means. It means, for example, that the PA, NP, NA, and MP segments circulating today are all derived from the Yamagata lineage. But what does the 1984 to 1987 part of this chart mean? Is it really true that at this time the majority or all of these segments were Victoria-type? If yes, does this mean that when Vic and Yam split the initial diversification was in PB1-PB2-HA and the PA, NP, NA, and MP segments were largely conserved during this time? If yes, should we really call these Victoria-type in 1984, or are they simply the ancestral type before the split occurred?

Does sampling bias affect the results of Figure 5? I believe we have enough influenza B sequences to reconstruct the post-2005 part of this chart. How much confidence do we have in 1995? 1985?

[trvrb]

The "genome counts" at the top of the figure are very helpful. I hadn't realized there was just one genome in each of the first three years. Impossible to get proportions from this. I'd suggest just dropping these first three years from the figure.

[evogytis]

Sure, dropping the first years sounds good. Also, if you run the same analysis using the 1600 genomes dataset the lineage ratios look quite consistent with what we have sampled in our 452 dataset. I'm considering adding some indicator to the current figure to show where the 1600 dataset ratio lies to discourage comments about sampling.

[evogytis]

Should be closed via 74f7209eb9dd191e624d4a8de71585ba2ebe7cdb.

[evogytis]

MBE Reviewer#2: "Figure 5: If I understand this figure correctly, the authors are using the BEAST MCC tree of each segment, looking at a particular point in the past, and counting the number of extant lineages that would be associated either with the original 1983 Yamagata virus or the original 1983 Victoria virus. I understand what the `recent past' part of this chart means. It means, for example, that the PA, NP, NA, and MP segments circulating today are all derived from the Yamagata lineage. But what does the 1984 to 1987 part of this chart mean? Is it really true that at this time the majority or all of these segments were Victoria-type? If yes, does this mean that when Vic and Yam split the initial diversification was in PB1-PB2-HA and the PA, NP, NA, and MP segments were largely conserved during this time? If yes, should we really call these Victoria-type in 1984, or are they simply the ancestral type before the split occurred?

Does sampling bias affect the results of Figure 5? I believe we have enough influenza B sequences to reconstruct the post-2005 part of this chart. How much confidence do we have in 1995? 1985?"

[evogytis]

I'm guessing the word lineages in Figure 5 is causing the continued confusion. Will change it to just sequences.