Currently, the beginning two paragraphs of Results 5 segments lose diversity and 3 segments maintain diversity are overly disconnected from the primary results. I would recommended basing the structure around figures. My current thoughts on figure order:
Labels are to emphasize conceptual separation, not actual sub-heads in manuscript
Phylogenetic investigation
This section approaches phylogenetic patterns of reassortment and establishes why segments differ in their level of diversity, i.e. introgression and fixation occurs in 5 of the segments, but not HA, PB1 and PB2.
Fig 1: Tree figure showing trees for all 8 segments as a grid
Fig 2: Current figure 3 (InfB_tmrcaOT_lines) that shows diversity within each segment not worrying about identifying reassortment per se and prompts the investigation (aha! H1, PB1 and PB2 are old, while other segments are younger).
Fig 3: Current figure 5 (InfB_betweenDiversity) that elaborates on the previous figure showing increasing distance between Vic and Yam in HA, PB1 and PB2.
Fig 4: Current figure 4 (InfB_LineageRatiosOverTime) that makes it clear that the reason diversity is being lost is because one lineage is taking over in 5 of the segments, but both lineages are being maintained in HA, PB1 and PB2.
Fig 5: Current figure 6 (RailroadPlotDated) that diagrams what's going on and further shows introgression in some segments and maintenance in others.
HA-PB1-PB2 gene complex
This section focuses on HA-PB1-PB2 association and tries to prove they are a gene complex
Fig 6: Current figure 2 (InfB_stateTime) to emphasize that HA, PB1 and PB2 are remaining together and reassortants don't last long.
Fig 7: Current figure 7
Fig 8: Current figure 8
Fig 9: Current figure 9 However, I would recommend turning this from a heat map to a bar chart matching the form of figures 7 and 8.
Currently, the beginning two paragraphs of Results 5 segments lose diversity and 3 segments maintain diversity are overly disconnected from the primary results. I would recommended basing the structure around figures. My current thoughts on figure order:
Labels are to emphasize conceptual separation, not actual sub-heads in manuscript
Phylogenetic investigation
This section approaches phylogenetic patterns of reassortment and establishes why segments differ in their level of diversity, i.e. introgression and fixation occurs in 5 of the segments, but not HA, PB1 and PB2.
InfB_tmrcaOT_lines) that shows diversity within each segment not worrying about identifying reassortment per se and prompts the investigation (aha! H1, PB1 and PB2 are old, while other segments are younger).InfB_betweenDiversity) that elaborates on the previous figure showing increasing distance between Vic and Yam in HA, PB1 and PB2.InfB_LineageRatiosOverTime) that makes it clear that the reason diversity is being lost is because one lineage is taking over in 5 of the segments, but both lineages are being maintained in HA, PB1 and PB2.RailroadPlotDated) that diagrams what's going on and further shows introgression in some segments and maintenance in others.HA-PB1-PB2 gene complex
This section focuses on HA-PB1-PB2 association and tries to prove they are a gene complex
InfB_stateTime) to emphasize that HA, PB1 and PB2 are remaining together and reassortants don't last long.