Are taxonomies networks?

One of the basic tenets of modern systematics is that taxonomies should be hierarchical. That is, we arrange things in a nested hierarchy, with decreasing similarity among the objects as we proceed towards the tip. Indeed, one of Darwin's arguments for his version of biological evolution was that specie splitting leads naturally to a hierarchical taxonomy.

However, it is clear that not everyone agrees with this idea. The web is full of things labelled "taxonomy" but which are clearly networks. I have gathered a few of them here for you.

The first example is from Business Insider UK, Everything you need to know about beer, in one chart. It seems to be quite informative.

An even more complex version, and thus much more network-like, is available at Pop Chart Lab: The magnificent multitude of beer. However, this is not labelled as a "taxonomy". Just as an aside, there is also A periodic table beer styles (an earlier version is here).

The next one is ubiquitous on the web, but appears to come from Charley Chartwell: A grand taxonomy of Shakespearean insults. It may give you some good ideas!

The next one also comes from Pop Chart Lab: The grand taxonomy of rap names.

Here is a version without the centre obscured, although it is no longer labelled as a taxonomy:

Next we have one from Stephen Wildish: The fish & chip taxonomy.

This final network is a bit more cheeky than the others. It is also from Stephen Wildish: A taxonomy of arse.

There are many other "taxonomies" out there, many of which are basically star trees, with very few being truly tree-like. Here is a simple "tree" taxonomy, which comes from Kate Turner: The taxonomy of my music. Unfortunately, I think that in reality it should probably be a network, like the others.

Beer family trees

Some time ago I wrote a blog post about The bourbon family forest, which contained a collection of trees that, rather than being genealogical trees, instead showed the corporate ownership of American whiskey.

Here is a similar arrangement for "the six companies that make 50% of the world's beer", produced by David Yanofsky at the Quartz blog. As before, the vertical axis is actually a time scale, but the trees are only marginally family trees in the genealogical sense. Note that there is a reticulation between two of the trees for the "Scottish & Newcastle" entry, although this was apparently followed immediately by a subsequent divergence.

Nevertheless, roughly the same sort of information could actually be presented as proper genealogies. Here is an example form Philip Howard's blog, restricted to American beer. Note that the genealogies refer to the joining of branches through time, rather than their splitting. There are two reticulation events, one of which also refers to the "Scottish & Newcastle" entry.

It is also worth noting the use of other types of network by Philip Howard, to look at:

• Visualizing ownership in the soft drink industry
• Concentration in the U.S. beer industry
• Concentration in the U.S. wine industry

Lager beer and phylogenetic networks

Beer and wine making have been known since ancient times, but both were 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, which 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.