If I understand the paper (I’ll admit it’s a bit beyond my level) then the twigs (or at leas the tips) are individuals sampled from what may or may not be two species. The test then is whether any of the clades identified in the tree are so far apart from each other they are unlikely to have arisen by chance (so represent species in the Simpson sense of “independently evolving lineages”)

The 4Ne bit comes from the population genetics. The set up is that on average a contiguous population will contain lineages that are 2Ne generations apart from each other (it sort of stands to reason than in a small population everyone is more closely related). As it happens, you only have a 5% chance of finding a lineage that goes back 4Ne generations within a contiguous population so that’s the cut they’ve used in this paper.

I guess they would argue that’s also the difference between their method and the Phylogenetic Species Concepts – rather than being monophyly + some diagnosable character it’s a cut off derived from population genetics.

Does that help at all?

I guess one thing I don’t fully understand is the “4 times this amount of generations” part… So, if Ne is the proportion of the population that are breeders, then do you need 4 times their number? Or 4 times the average amount of offspring they produce (a generation)?

And I understand from the blogcast that this was developed more for non-sexually reproducing organisms, but do you think this has any application for very small meta-populations, like with endangered species?

Thanks for humoring me.

“I urge readers to use the general term “K/θ method” for this method, as opposed to the “4x rule” which can be confused with arbitrary or empirically determined ratios. A better name for the 4x rule might be the K/θ(0.95) criterion. Those who wish to use a different confidence interval would be free to use, for example, K/θ(0.90) or K/θ(0.99). The appropriate K/θ ratio would be determined jointly by the chosen confidence interval and the sample size.”

I downloaded the article before this comment was posted a week ago, or else I would used this terminology which is more clear.

The 4x rule means that at a 95% level of certainty, this would be the phylogenetic distance that 2 clades would need to be apart to be sufficiently diverged. We didn’t get into the math, but this figure from the paper visually shows the model. The estimate of “within-clade” genetic diversity is Theta and is estimated, by doing some equation rearranging, 2Neu, where Ne is the effective population size and u is the mutation rate of the gene. So if Ne is the number of breeding individuals in a population in a generation, 4 times this amount of generations is what the authors argue should be sufficient time for the two clades to diverge. Does this help or confuse you more?