Monday, April 16, 2018

Networks in the news, at last

Phylogenetic networks do not always fare very well in the traditional media. The general public has enough troubles dealing with a phylogenetic tree, let alone networks. For example, many people still consider that Darwin claimed that monkeys are our ancestors (a chain-based relationship) rather than our cousins (a tree-based relationship) — who knows what they must think about humans inter-breeding with Neandertals (a network-based relationship).

Nevertheless, a few news reports about a recent network-based paper have suggested that the situation might be improving.

The paper in question is:
Úlfur Árnason, Fritjof Lammers, Vikas Kumar, Maria A. Nilsson, Axel Janke. Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Science Advances 4: eaap9873.
This paper details extensive genomic admixture among six species of Baleen whales. The phylogenetic scenarios involving gene flow cannot be represented by a tree, of course, so the authors include the following set of networks (along with a Median network).

News reports have appeared in at least two places, reporting on this paper, that discuss the difference between networks and "Darwinian trees", and do quite a good job of it.

For example, this quotation is from the New York Times ("Baleen Whales intermingled as they evolved, and share DNA with distant cousins"):
The relationships are so complicated, however, that the senior researcher Axel Janke said "family tree" is too simple a metaphor. Instead, the species, all part of a group called rorquals, have evolved more into a network, sharing large segments of DNA with even distant cousins. Scientists expressed surprise that there had been so much intermingling of baleen whales, given the variety of sizes and shapes.
This quotation is from Popular Science ("A new study on whales suggests Darwin didn't quite get it right"):
Evolutionary network analysis takes the tree metaphor and turns it into a complex web, which acknowledges the different kinds of familial connections shown by whole-genome sequencing. Comparing the whole genomes of rorquals shows that genetics is much more fluid than the Darwinian “tree” model, Janke says.
"Gene flow and hybridization is more common than biologists usually think," Janke says. Analysis of the rorquals’ genes shows that they've interbred in different ways at various times in their evolutionary history. This doesn't make much sense if you rely only on Darwin's model, where branches of the family tree never touch again after they separate.
I think that these give us all a reason for optimism.