TableS1.The GenBank Accession numbers of the sequences used in Figures 1 and 2.

Genes / Name / Accession number / Name / Accession number
PB2 / A/blue winged teal/LA/B228/1986
A/turkey/SD/7034/1986
A/mallard/Ohio/171/1990
A/green-wingedteal/Ohio/430/1987
A/swine/Ohio/75004/04
A/swine/OH/511445/2007
A/Iowa/CEID23/2005
A/Mexico/InDRE4114/2009
A/California/04/2009
A/Texas/04/2009
A/New York/1669/2009 / EU743313
EU743174
CY012807
CY011047
EU409953
EU604691
DQ889682
GQ132138
FJ969516
FJ969525
CY039900 / A/mallardduck/ALB/322/1988
A/mallard/ALB/201/1998
A/mallard/Ohio/118/1993
A/black duck/Ohio/95/1993
A/swine/Korea/CAN01/2004
A/swine/Korea/CAS08/2005
A/Texas/09/2009
A/California/05/2009
A/Canada-ON/RV1527/2009
A/Arizona/02/2009 / CY004538
CY004514
CY018892
CY015450
EU798918
EU798919
GQ117027
FJ966955
FJ998205
GQ117076
PB1 / A/turkey/Ontario/31232/2005(H3N2)
A/turkey/OH/313053/2004(H3N2)
A/swine/Ohio/75004/04
A/swine/Korea/CAS08/2005
A/swine/OH/511445/2007
A/swine/Ohio/C62006/06
A/New York/18/2009
A/Wisconsin/10/98 / DQ469996
EU735824
EU409954
EU798899
EU604692
EU409959
FJ984353
AF342823 / A/Arizona/02/2009
A/California/04/2009
A/Mexico/InDRE4487/2009
A/Minnesota/02/2009
A/Texas/05/2009
A/Indiana/09/2009
A/Canada-NS/RV1527/2009
A/Iowa/CEID23/2005 / GQ117075
FJ966080
FJ998226
GQ117069
FJ969522
GQ117093
FJ998225
DQ889683
PA / A/blue-winged teal/Alberta/141/1992
A/duck/NJ/7717-70/1995
A/turkey/MO/21939/1987
A/pintail duck/ALB/238/1979
A/black duck/Ohio/95/1993
A/mallard duck/ALB/322/1988
A/mallard/Ohio/171/1990
A/duck/NY/13152-13/1994
A/turkey/SD/7034/1986
A/mallard/Maryland/350/2002
A/Texas/04/2009
A/Michigan/02/2009
A/New York/11/2009
A/New York/18/2009
A/Canada-ON/RV1527/2009 / CY004543
EU026115
EU743148
CY004487
CY015448
CY004536
CY012805
EU026107
EU743172
CY032210
FJ981619
GQ117109
FJ984346
FJ984354
FJ998224 / A/mallard/MD/11/2003
A/mallard/Alberta/267/1996
A/mallard/ALB/201/1998
A/muscovy duck/NewYork/21211-5/2005
A/California/04/2009
A/California/07/2009
A/Mexico/InDRE4487/2009
A/Indiana/09/2009
A/Canada-NS/RV1535/2009
A/Texas/09/2009
A/Iowa/CEID23/2005
A/swine/Minnesota/SG-00240/2007
A/swine/Korea/CAS08/2005
A/swine/Saskatchewan/18789/02 / EU980513
CY014566
CY004512
CY029846
FJ966081
FJ966977
FJ998223
GQ117095
FJ998222
GQ117029
DQ889684
CY035435
EU798879
AY619956
HA / A/swine/Korea/CY08/2007(H1N2)
A/Swine/Ohio/891/01(H1N2)
A/Turkey/MO/24093/99(H1N2)
A/California/04/2009
A/California/05/2009
A/Texas/05/2009
A/California/06/2009
A/NewYork/12/2009
A/Ohio/07/2009 / EU798788
AF455675
AY038014
FJ966082
FJ966952
FJ966959
FJ966960
FJ984337
FJ984397 / A/swine/Minnesota/00194/2003(H1N2)
A/swine/Kansas/00246/2004(H1N2)
A/Swine/Indiana/9K035/99_(H1N2)
A/swine/Minnesota/1192/2001(H1N2)
A/California/07/2009
A/New York/19/2009
A/Denmark/513/2009
A/NewYork/23/2009 / EU139830
EU139831
AF250124
EU139828
FJ966974
FJ969509
FJ982430
FJ984364
NP / A/Mexico/InDRE4487/2009
A/California/04/2009
A/California/08/2009
A/SouthCarolina/09/2009
A/California/05/2009
A/swine/OH/511445/2007
A/Swine/Wisconsin/457/98
A/swine/Iowa/17672/1988
A/swine/Iowa/24297/1991
A/swine/Memphis/1/1990 / FJ998217
FJ969512
FJ984366
GQ117052
FJ966953
EU604694
AF222776
CY022336
CY027158
CY035073 / A/Minnesota/02/2009
A/NewYork/12/2009
A/NewYork/06/2009
A/Michigan/02/2009
A/Wisconsin/10/98
A/swine/Korea/CAS08/2005
A/swine/Quebec/5393/91
A/swine/Shanghai/1/2005
A/turkey/NC/19762/1988 / GQ117068
FJ984336
FJ984341
GQ117107
AF342819
EU798839
AF397199
EU502887
EU735789
NA / A/California/05/2009
A/New York/06/2009
A/New York/12/2009
A/Mexico/InDRE4487/2009
A/Canada-NS/RV1527/2009
A/Ohio/07/2009
A/Michigan/02/2009
A/swine/Italy/53949/2004
A/swine/Hungary/19774/2006
A/swine/Zhejiang/1/2007
A/Swine/Spain/50047/2003
A/swine/Ratchaburi/NIAH550/2003
A/swine/England/WVL16/1998 / FJ966956
FJ984340
FJ984335
FJ998214
FJ998213
FJ969534
GQ117108
EU045388
FJ798780
FJ415611
CY009894
AB434298
CY037954 / A/Texas/04/2009
A/Canada-ON/RV1527/2009
A/Indiana/09/2009
A/Netherlands/602/2009
A/California/04/2009
A/Kansas/02/2009
A/swine/Belgium/1/1998
A/swine/Chonburi/06CB2/2006
A/swine/Denmark/WVL9/1993
A/swine/Spain/WVL6/1991
A/swine/Scotland/WVL17/1999
A/swine/England/WVL7/1992 / FJ966981
FJ998215
GQ117094
CY039528
FJ966084
GQ117058
FJ805963
EU296606
CY038025
CY038001
CY037962
CY038009
M / A/swine/Chonburi/NIAH589/2005
A/swine/Hungary/19774/2006
A/swine/Spain/53207/2004
A/swine/Zhejiang/1/2007
A/swine/Belgium/1/1998
A/swine/Belzig/2/2001
A/Canada-NS/RV1535/2009
A/Texas/07/2009
A/PaisVasco/GP20/2009
A/New York/06/2009 / AB434323
FJ798779
CY010581
FJ415612
FJ805964
DQ186976
FJ998210
GQ117090
FJ985760
FJ984338 / A/California/05/2009
A/California/06/2009
A/Castilla-LaMancha/GP13/2009
A/California/10/2009
A/Valencia/GP4/2009
A/Texas/05/2009
A/Texas/06/2009
A/Michigan/02/2009
A/Canada-ON/RV1527/2009
A/Thailand/271/2005 / FJ966954
FJ966962
FJ985750 FJ969510
FJ985755
FJ981608
FJ984381
GQ117111
FJ998212
EF101750
NS / A/turkey/IA/21089-3/1992
A/turkey/NC/19762/1988
A/Texas/09/2009
A/Texas/05/2009
A/Texas/15/2009
A/Minnesota/02/2009
A/Valencia/GP4/2009
A/Canada-NS/RV1535/2009
A/California/04/2009
A/Castilla-LaMancha/GP13/2009
A/swine/Iowa/17672/1988
A/swine/Maryland/23239/1991
A/swine/Alberta/56626/03
A/swine/Iowa/3/1985 / EU743163
EU735790
GQ117030
FJ981611
GQ122093
GQ117072
FJ985757
FJ998219
FJ969514
FJ985750
M80964
CY022481
DQ280200
CY022329 / A/Denmark/513/2009
A/NewYork/18/2009
A/California/14/2009
A/Canada-ON/RV1527/2009
A/Nebraska/02/2009
A/California/06/2009
A/Kansas/03/2009
A/Iowa/CEID23/2005
A/Ohio/3559/1988
A/swine/OH/511445/2007
A/Swine/Wisconsin/458/98
A/swine/Shanghai/1/2005
A/turkey/NC/19762/1988
A/turkey/IA/21089-3/1992 / FJ982433
FJ984349
GQ117038
FJ998221
GQ117106
FJ971074
GQ117061
DQ889685
CY024929
EU604696
AY619978
EU502889
EU735790
EU743163