Wednesday, May 7, 2014

Lager beer and phylogenetic networks

Beer and wine making have been known since ancient times, but was usually a hit-or-miss affair. However, beer brewing gradually changed during the Middle Ages in Europe to produce a consistent ale-type beer. The process is carried out by the yeast Saccharomyces cerevisiae, which is also involved in producing wine and leavened bread.

Lager beer, on the other hand, was first brewed in the 15th century in Bavaria (now part of Germany), and it has since become the most popular type of beer worldwide. Lager is bottom fermented (versus top-fermented for ale), and the fermentation is carried out at a lower temperature (< 10 °C versus 15-25 °C). It produces a "smooth, crisp, fruity, and clean" beer as opposed to the "robust, hearty and fruity" ale beer.

Lager beers are made using a yeast known as Saccharomyces pastorianus (also known as Saccharomyces carlsbergensis). This is a domesticated species that depends on humans for its propagation, and it is an allotetraploid hybrid. For a long time, we have known that half of the genome came from the ale yeast Saccharomyces cerevisiae, but the other half came from an unidentified species. In 2011, Libkind et al. (Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proceedings of the National Academy of Sciences of the USA 108: 14539-14544) identified the missing parent yeast as the previously unknown species Saccharomyces eubayanus, which grows on Nothofagus (Southern Beech) trees in Patagonia (in Argentina).

Lager was developed when the Bavarians started to brew and store their beer in caves or cellars and kept it at a constant cool temperature. This required a yeast that could tolerate the colder temperatures, and it is apparently this component that Saccharomyces eubayanus contributes to the Saccharomyces pastorianus hybrid. Precisely how it got from Patagonia, at the southern tip of South America, to south-eastern Germany is not clear, but perhaps some were carried on the feet of fruit-flies.

Since we are dealing with an allotetraploid hybrid, and thus reticulate evolution, a phylogenetic network would be the appropriate means to illustrate its origins. This has recently been provided by Peris et al. (2014. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Molecular Ecology 23: 2031-2045). They report that:
genetically diverse strains of S. eubayanus are readily isolated from Patagonia, demonstrating that the species is well established there. Analyses of multilocus sequence data strongly suggest that there are two diverse and highly differentiated Patagonian populations. The low nucleotide diversity found in the S. eubayanus moiety of hybrid European brewing strains suggests that their alleles were drawn from a small subpopulation that is closely related to one of the Patagonian populations ... These findings show how genetically diverse eukaryotic microbes can produce rare but economically important hybrids with low genetic diversity when they migrate from their natural ecological context.

The authors actually present two networks, the first of which is shown here. It is an unrooted supernetwork derived from the the maximum-likelihood trees of each of eight nuclear genes. It shows the network of samples from three named Saccharomyces species, along with expanded views of the two Patagonian populations. Isolates W34/70 and BCS1503 are from the lager yeast, Saccharomyces pastorianus, which in the network are related to the Patagonia B population. The three Saccharomyces bayanus samples (beer contaminants) are hybrids between Saccharomyces eubayanus and Saccharomyces uvarum.

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