We had journal club today, and I realised that something that I had always considered quite obvious and logical is not as obvious and logical to everybody else. The question here is: how old is a species?
If you are like me, you will visualise the phylogenetic tree of the species and its closest relatives, point to the moment where it diverged from its sister group, and say that that is its age. See the following diagram:
We know today of the existence of species A, C and D, and if we reconstructed the phylogeny I would say that the divergence time of A on the one side and the ancestor of C and D on the other side, marked with the black line and the number 1, is the age of species A.
However, there is a little snag: What if there were side branches on the tree of life that we do not know about because they are now extinct? In the hypothetical case above, there existed a species B for some time but then it died out. So really the age of species A should be the divergence time from B, indicated with the purple line and the number 2. But if we only know about A, C and D, we can at least say that A is at the most as old as indicated by the black line.
So far so good. What I learned today is that there are apparently people who believe that the age of a species is where the gene copies it is carrying or the family lineages inside it coalesce back in time. This is indicated by the red line and the number 3: the yellow gene tree shows that all extant gene copies (of that gene) in species A are derived from an ancestral copy that existed at time 3.
This time would often be much closer to the present than times 2 and 3. In the case of us humans, we are usually inferred to have diverged from the chimpanzee lineage a few million years ago, but the last female and male common ancestors of all of humanity - the individuals from whom we have all inherited our mitochondria and Y chromosomes, respectively - have been inferred to have existed a few ten to hundred thousand years ago. And indeed some people seem to assume that that is then the age of our species. (See also my earlier dissection of the Doomsday Argument.)
When I was reminded of this concept today I couldn't believe that this would make sense to any biologist. Mike Crisp pointed out the first major problem: this coalescence point constantly moves through time as gene lineages and family lineages proliferate and die out again. As one can see even in my little diagram above, there were several earlier times at which the same would have been true. So how can the age of the same species constantly be corrected downwards as it gets older?
Worse, if speciation events are spaced closely in time and effective population sizes are large, it is well possible that coalescence time might actually be in an ancestor of species A instead of itself; this is known as incomplete lineage sorting or ancestral polymorphism. In other words, species A would then be older than its existence as an independent lineage. Surely that is immediately recognisable as nonsensical.
However, Mike also pointed out that (as I would add: in cases where it is after the lineage divergence time that we can infer), this coalescence point provides a lower limit on the age of a species. So it must then at least be as old as that, and it is at most as old as the divergence time from its living relatives.