Supplemental Information Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian In fl uenza Virus

[1]  Chase W. Nelson,et al.  SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data , 2015, Bioinform..

[2]  R. Sebra,et al.  Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection , 2015, mBio.

[3]  Chase W. Nelson,et al.  Within-host nucleotide diversity of virus populations: insights from next-generation sequencing. , 2015, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[4]  D. Burke,et al.  Circulating avian influenza viruses closely related to the 1918 virus have pandemic potential. , 2014, Cell host & microbe.

[5]  Chase W. Nelson,et al.  High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population , 2014, PloS one.

[6]  Chase W. Nelson,et al.  Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H 5 N 1 influenza viruses , 2013 .

[7]  A. Futschik,et al.  PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals , 2011, PloS one.

[8]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[9]  R. Webster,et al.  "Ambisense" approach for the generation of influenza A virus: vRNA and mRNA synthesis from one template. , 2000, Virology.

[10]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.