Did All Species Arise about 200,000 Years Ago?

[swamidass (S. Joshua Swamidass)]

So, @vjtorley, this paper equivocates several things, or at least it seems so. I would go so far as to say that is methodologically flawed in the biorxiv form. I’d hope that the authors correct it in review.

1. They equivocate TMRCA with species age. That is just false. To map to other conversations we have, they are essentially reproducing the well known results that Mito-Eve appears to arise between 200 kya and 100 kya, but this in itself tells us precisely zero information about when Homo sapiens arise.
2. Mitochondrial clocks require a great deal of effort to calibrate and different species will have different rates. This is very difficult to do, and they have not done so adequately (or at all?). This means that they are equivocating “diversity” for “TMRCA”. They should have instead reported the substitution rate distance, not the TMRCAs, as the TMRCAs are certainly not definitive. The fact of the matter is that we do not have good estimates of mitochondrial mutation rates in most species.
3. They appear to be using extant population size instead of historical population size. That is not warranted. The fact that humans have a few billion people in recent history, does not mean anything regarding our ancient history. The fact of the matter is that we do not have good estimates for past populations sizes.
4. To get a TMRCA we also need to account for the degree of selection at this locus, because it is clearly not neutral. This was not adequately accounted for, and once again, will affect the results.
5. They wildley over interpret measurements from a single loci. Such an effort is deeply flawed. For example, by mitochondria, Neandertals and Sapiens are different (but not more different than two chimps!) but when we look at autosomal genome, we see evidence of interbreeding. This directly contradicts the conclusions and reasoning of the paper.

So, to be clear, this seems to be very problematic study, with results that are wildly overstated. They have a provocative title, but are no way able to justify it.

@vjtorley

(i) the article says that most species today, including Homo sapiens , are between 100,000 and 200,000 years old. However, recent discoveries have pushed back the origin of Homo sapiens to 300,000 years ago, so it seems we’re an exception to the general trend. Or are the authors suggesting that fossil identifications of species are unreliable, and that only identifications which are based on mitochondrial DNA should be trusted?

It hard to describe this as anything other than an error of false equivolance. They take a very unreliable estimate of TMRCA, and then equivocate that “When a species arises.” Such a jump is just false. That is not correct or valid. TMRCA and speciation are not the same thing. It ignores everything else.

It seems to be falling hard for the streetlight fallacy. We can’t measure A, but we can measure B, so lets pretend by measuring B we know what A is.

http://discovermagazine.com/2010/jul-aug/29-why-scientific-studies-often-wrong-streetlight-effect
The fundamental error here is summed up in an old joke scientists love to tell. Late at night, a police officer finds a drunk man crawling around on his hands and knees under a streetlight. The drunk man tells the officer he’s looking for his wallet. When the officer asks if he’s sure this is where he dropped the wallet, the man replies that he thinks he more likely dropped it across the street. Then why are you looking over here? the befuddled officer asks. Because the light’s better here, explains the drunk man.

They need to get out of the genetic streetlight, to consider a whole ton of other things. Their response would likely be “but that is hard!” to which most scientists would say: “Yes, science is hard. Get to it.”

@vjtorley

(ii) From what I gather, the average lifetime of a species seems to be around 5 million years. So if, as the article says, most species are between 100,000 and 200,000 years old, then even today, it’s still pretty early on in their lifetimes. Curious.

Except they are not measuring the age of species. They are measuring TMRCA at a single locus, without even calibrating their clock.

@gbrooks9

We aren’t looking at an average life cycle for all species at all times in Earth’s history… we are looking at a very special time in the history of the Earth … which produces speciation patterns based on global ice ages sweeping in, and knocking everybody’s card tables to the ground!

Absolutely correct @gbrooks9. The equivocation between TMRCA and when a species arises is really poor. I’d be surprised and disappointed if they got that past peer review.