Bayesian phylogenetic analysis of the haemagglutinin and neuraminidase proteins of influenza A virus demonstrates that their respective most recent common ancestors (MRCAs) both existed approximately 1000years ago. Most of the bifurcations within the haemagglutinin and neuraminidase phylogenetic trees occurred within a time window that can be dated with 95% confidence to the years 1411-1932 of the Common Era (AD) for haemagglutinin and 1366-1874 AD for neuraminidase. This subtype diversification episode is temporally congruent with the "Little Ice Age", a period of climatic cooling over the northern hemisphere. Furthermore, Bayesian probability mean ages for the bifurcation points within the haemagglutinin tree indicate two bursts of diversification from 1672 to 1715 AD and from 1825 to 1868 AD. The first of these follows in the wake of the coldest epoch in the Little Ice Age, and the second overlaps a later cooling episode. Since climate change is known to affect migration patterns in the reservoir host of influenza A, the aquatic wildfowl, and allopatric cladogenesis following population disruption is well supported in the evolutionary literature, a mechanism is proposed linking the Little Ice Age to influenza subtype diversification via ecological disruption of the wildfowl annual cycle. The suggestion that past climate change has impacted on influenza evolution implies that current global warming may cause a further burst of influenza subtype diversification with possible serious epidemiological consequences becoming apparent in the 22nd and 23rd centuries.
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