the oldest y chromosome that wasn't

The divergence time of the most recent common ancestor (TMRCA) of all Y chromosomes was estimated to be 338,000 years ago, and possibly even 581,000 years ago

On March 7, 2013, Mendez and colleagues reported a most amazing discovery: an ancient Y chromosome that is basal to all other human Y chromosomes in the phylogenetic tree.

Mendez and colleagues were not at all coy about their estimate:

“In contrast to the estimates of all previous studies, our estimate of the Y chromosome TMRCA predates both that of known mtDNA lineages and of the likely time of origin of AMHs on the basis of current fossil evidence.” (Mendez et al. 2013)

“…we should not be surprised that the Y chromosome genealogy does not match the currently accepted phylogeny of human populations…” (Mendez et al. 2013)

Or the implication for our species…

Hammer, M. F. 2013. Human Hybrids. Scientific American. 308:66-71.

The media went WILD!

We soon learned that…

But the worst part was that…

… and

Could it all be wrong?

Estimating the age of a population requires us to consider three variables:

1)Generation time.2)Mutation rate (number of mutations/generation time).3)Number of mutations.

Let us assume that a hypothetical tribe has a generation time of 1 year and a mutation rate of 0.1 mutations per generation. If we find 10 mutations in the Y chromosome of one individual, we can easily calculate that the age is:

1 x 10/0.1 = 100 years old

… and a longer generation time (say, 2 instead of 1)2 x 10/0.05 = 400 years old.

We can easily make the age look older by using a slower mutation rate (say, 0.05 instead of 0.1)

1 x 10/0.05 = 200 years old.

… and miscount the number of mutations (say, 20 instead of 10)

2 x 20/0.05 = 800 years old!

In a similar manner, the TMRCA estimate by Mendez et al. (2013) and Hammer (2013) was reached through inadequate statistical and analytical methods, each of which contributed to its inflation, as we shall show in the following.

We will also show that the model the authors invented has devastating implications for our species as it creates a space-time paradox that may mark our (retroactive) end!

"How did Mendez et al. (2013) misled thee? Let us count the ways...”

With profuse apologies to Elizabeth Barrett Browning

1. The authors derived the Y-specific substitution rate from autosomal mutation rates instead of using previously inferred Y-specific substitution rates.

Why is it wrong?

1) Substitution rate on the Y chromosome is NOT linearly related to the

autosomal rate.

2) The mutation rates were calculated for one generation and are NOT equal

to the substitution rates from our most ancient ancestor to these days.

Remember our hypothetical example?

Slow mutation rate will increase the age of the Y chromosome.

2. They used a generation time of 40 years.

Why is it wrong?

Generation time in humans was never 40 years!

Remember our hypothetical example?

Higher generation time will increase the age of the Y chromosome.

3. They used sequences of unequal lengths in the comparison between the newly found lineage A00 and the recognized basal A0.

The authors sequenced 240 kb of the newly found chromosome (A00) but only reported 75% of it. In their comparison, mutations were counted on all the 240 kb of the A0 chromosome but only along portion of the A00 chromosome.

Why is it wrong?

A0

A00

???

Because that’s cheating (or at least a deep-tissue massaging of the data)!

Remember our hypothetical example?

Miscounting the number of mutations will increase the age of the Y chromosome.

The conclusions of Mendez et al. (2013) create a space-time paradox.

To make the new Y chromosome look even older, Mendez et al. (2013) invented a new branch of statistics:

1. Confidence intervals were used for predictions instead of prediction intervals.2. 90% confidence intervals were deemed sufficient instead of the customary 95% or 99%. 3. The “median” and “standard deviation” of the five numbers (9, 10, 11, 15, and 26) were calculated as 14.2 and 3.12, respectively, instead of 11 and 6.98 in typical algebra.4. Normal distribution was deduced on the basis of 5 data points.

The conclusions of Mendez et al. (2013) create a space-time paradox.

Correcting these errors yields a most remarkable finding!

The number of mutations per generation has negative values. That is, some events are predicted to have occurred in the future. (Grammar is not the only thing being abused by their work.)

Therefore, a possible scenario is that the most ancient man in the world has not yet been born.

In principle, thus, the mother of the unborn most ancient male Homo sapiens may decide upon reading the paper by Mendez et al (2013) not to conceive. Such a decision may spell the retroactive end of our species.

From: Back to The Future I (1985)

Mendez et al. (2013) may become very rich by selling their findings to Robert Zemeckis & Bob Gale to serve as the basis for Back to the Future IV.

Fortunately, a normal distribution cannot be deduced from 5 data points, so humanity may be safe...

Using traditional methodology, we estimated the Y chromosome age to be:

208,300 years (95% CI = 163,900-260,200).

Slightly more ancient than previous estimates… but still in the range of the logical.

In summary

We have shown that consistently throughout their examination, Mendez et al. (2013) have used assumptions, approximations, numerical miscalculations, and data manipulation that inflated their final estimate.

Our estimate excludes the possibility of introgression with most ancient hominin species.

Our paper:

The “Extremely Ancient” Chromosome that Isn’t: A Forensic Bioinformatics Investigation of Albert Perry’s X-degenerate Portion of the Y Chromosome

Eran Elhaik1, Tatiana V. Tatarinova2, Anatole A. Klyosov3, and Dan Graur4

 1 Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2103, USA2 Department of Pediatrics, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA3 The Academy of DNA Genealogy, Newton, MA 02459, USA4 Department of Biology & Biochemistry, University of Houston, Houston, TX 77204-5001, USA

was published in the European Journal of Human Genetics.

Relief: Adam has never engaged in zoophilic relationships with other species.