Doubts About Accuracy of Genetic Dating Techniques

[Laura]

Ancient Penguin DNA Raises Doubts About Accuracy of Genetic Dating Techniques

PhysOrg
Tue, 10 Nov 2009

Penguins that died 44,000 years ago in Antarctica have provided extraordinary frozen DNA samples that challenge the accuracy of traditional genetic aging measurements, and suggest those approaches have been routinely underestimating the age of many specimens by 200 to 600 percent.

In other words, a biological specimen determined by traditional DNA testing to be 100,000 years old may actually be 200,000 to 600,000 years old, researchers suggest in a new report in Trends in Genetics, a professional journal.

The findings raise doubts about the accuracy of many evolutionary rates based on conventional types of genetic analysis.

"Some earlier work based on small amounts of DNA indicated this same problem, but now we have more conclusive evidence based on the study of almost an entire mitochondrial genome," said Dee Denver, an evolutionary biologist with the Center for Genome Research and Biocomputing at Oregon State University.

"The observations in this report appear to be fundamental and should extend to most animal species," he added. "We believe that traditional DNA dating techniques are fundamentally flawed, and that the rates of evolution are in fact much faster than conventional technologies have led us to believe."

The findings, researchers say, are primarily a challenge to the techniques used to determine the age of a sample by genetic analysis alone, rather than by other observations about fossils. In particular, they may force a widespread re-examination of determinations about when one species split off from another, if that determination was based largely on genetic evidence.

For years, researchers have been using their understanding of the rates of genetic mutations in cells to help date ancient biological samples, and in what's called "phylogenetic comparison," used that information along with fossil evidence to determine the dates of fossils and the history of evolution. The rates of molecular evolution "underpin much of modern evolutionary biology," the researchers noted in their report.

"For the genetic analysis to be accurate, however, you must have the right molecular clock rate," Denver said. "We now think that many genetic changes were happening that conventional DNA analysis did not capture. They were fairly easy to use and apply but also too indirect, and inaccurate as a result."

This conclusion, researchers said, was forced by the study of many penguin bones that were well preserved by sub-freezing temperatures in Antarctica. These penguins live in massive rookeries, have inhabited the same areas for thousands of years, and it was comparatively simple to identify bones of different ages just by digging deeper in areas where they died and their bones piled up.

For their study, the scientists used a range of mitochondrial DNA found in bones ranging from 250 years to about 44,000 years old.

"In a temperate zone when an animal dies and falls to the ground, their DNA might degrade within a year," Denver said. "In Antarctica the same remains are well-preserved for tens of thousands of years. It's a remarkable scientific resource."

A precise study of this ancient DNA was compared to the known ages of the bones, and produced results that were far different than conventional analysis would have suggested. Researchers also determined that different types of DNA sequences changed at different rates.

Aside from raising doubts about the accuracy of many specimens dated with conventional approaches, the study may give researchers tools to improve their future dating estimates, Denver said.

 

[Laura]

Redefining Man's Age

R Sivanithy
Business Times
Fri, 15 Oct 1999

Ever wondered about how old Man is?

Most scientists would reply that modern Man probably appeared around 100,000 years ago, the culmination of a long-drawn process of Darwinian evolution which begun several million years ago. This is the dominant paradigm, one that's taught in schools and universities and one which itself is the crystallisation of the efforts of researchers in the 140 or so years since Darwin's Origin of Species was published in 1859.

But just how accurate is this date? What if a piece of irrefutable evidence turns up which pushes back this figure significantly?

On July 8, The Straits Times ran a report that Australian researchers had unearthed stone artefacts on Flores, an Indonesian island west of Timor, which showed that boats which could be steered and propelled fairly sophisticatedly were in use 840,000 years ago.

The Flores finding obviously doesn't fit in with what the rest of archaeology says since communication had to be fairly sophisticated in order to build boats like these. But although this in itself is troubling, it doesn't necessarily upset the apple-cart if it's a one-off, or a completely isolated case. The trouble is, it isn't. Shaking current wisdom: The Flores artefacts are actually the latest in a long list of finds stretching back hundreds of years that cast serious doubt on current thinking about Man's age. The entire record of these findings can be found in a massive, 900-page volume entitled Forbidden Archaeology: The Hidden History of the Human Race that was published some six years ago.

Authors Michael Cremo and Richard Thompson are devotees and scholars of India's Vedic scriptures which say that Man -fully evolved homo sapiens and not the other members of the homo genealogies -is much older than is currently thought.

(In anthropological nomenclature, modern Man is more accurately named homo sapiens sapiens, which literally means "double wise man" to emphasise his intelligence. This is to distinguish him from say the Neanderthals, known as homo sapiens neanderthalensis, who may be from the same lineage (although this is disputable) but is thought to lack the same level of intelligence (again, this may be disputed)).

Together with other Hindu traditions, the Vedas are believed to have been brought to India by "Aryan" migrants from the shores of the Caspian Sea, cousins of the Indo-Europeans who were the Hittites of Asia Minor (today's Turkey) and of the Hurrians of the upper Euphrates River.

These migrations are believed to have taken place in the second millennium BC and the Vedas were held to be not of human origin, having been composed by the gods themselves in a much more distant previous age. In time, the various components of the Vedas and the auxiliary literature that derived from them (the Mantras, Brahmanas) were augmented by the non-Vedic Puranas (ancient writings) and the great epic tales of the Mahabharata and Ramayana.

In the Puranas, the conventional view of linear time is rejected. Instead, cyclical or episodic time is postulated, with 3,600-year cycles and multiples thereof being the most important.

Cremo and Thompson propose that the Puranic view of time and history predicts "a bewildering mixture of hominid fossils, some anatomically modern and some not, going back tens and even hundreds of millions of years and occuring in locations all over the world".

"It also predicts a more numerous but similarly bewildering mixture of stone tools and artifacts, some showing a high level of technical ability and others not."

They set out to see if they could validate these assertions and the fruits of their efforts are, in a word, astonishing. There are fossilised human footprints found in volcanic ash in Laetoli, Tanzania, dated to 3.6 million years, anatomically modern human skeletons found in Europe dating to the Middle Pliocene (five million years) and similar skeletons dating to Early Pliocene in Africa, Java and South America, Italy and England.

There are advanced stone tools in Europe dating to the Oligocene era (38 million years), Californian tools dating to Pliocene, South America and Asia and numerous cases of carved mammal bones presumably for decorative purposes dating to the Pliocene and Miocene (25 million years) eras.

Most of these and other anomalous findings were published in respected academic journals like the Journal of the Royal Anthropological Institute of Great Britain and Ireland and the American Journal of Physical Anthropology, yet are not public knowledge because of what the authors describe as a "knowledge filter". Against dissent: In short, the hypothesis is that there exists a prejudice against incongruous evidence that doesn't fit the dominant paradigm. This results in researchers ignoring and ultimately forgetting that such evidence exists.

Since the archaeological community has already accepted a certain view of Man's age, then it became unfashionable and in some cases, too dangerous, to challenge this view.

As a result, evidence which agrees with the dominant theory is readily accepted but that which doesn't is subjected to much more rigorous tests. The outcome is usually rejection and the researchers often face ridicule from their peers.

Predictably, Cremo and Thompson's book has been met with derision and criticism by a large part of the academic community, yet by the same token, there's also been enough acceptance from mainstream archaeologists to suggest that it should be taken seriously.

As the authors argue, it would be intellectually dishonest to ignore hundreds of contradictory findings that cast severe doubt on a current theory and yet, that is precisely what postmodern archaeology is guilty of today.

The points raised by the authors are bold and controversial. They make no attempt to mask their religious leanings but in reality, the evidence they have amassed through their eight-year search for the truth has no religious bias whatsoever and can and should be examined purely from the scientific point of view.

More importantly however, if what the authors assert can be taken as a realistic description of the state of archaeology today, then the Flores findings -like the hundreds of others before it -will quickly disappear into obscurity. Bad enough that Man's evolutionary history is already heavily shrouded in mystery but if this sort of suppression continues, things can only get worse.

 

[shijing]

I had no idea about this:

In the Puranas, the conventional view of linear time is rejected. Instead, cyclical or episodic time is postulated, with 3,600-year cycles and multiples thereof being the most important.

Isn't that interesting, given what has been said about the cycle of the comet cluster!...

As an aside, Flores is interesting for all sorts of reasons -- besides what is mentioned in this article, there is there is also a substantial history of pygmies, both human and animal (the human descendants in western Flores are still quite small, often being less than five feet tall).

Cremo et al's collected evidence is pretty interesting as well, although I think Laura mentioned in another thread that his dates have to be taken with a grain of salt also because of the C-14 problem. 840,000 years ago is quite a stretch further than the 309,000 years ago when we are supposed to have arrived on the scene -- unless our apelike predecessors were quite sophisticated.

 

[Voyageur]

Laura thanks for initiating this thread as indirectly you have spoken much about these issues in your books and writings. Also, you reminded me of your prior recommendation, as I purchased this book, Forbidden Archaeology: The Hidden History of the Human Race, which is a fascinating archaeological record of anomalies swept under the rug so to speak in effort to keep the apple cart on track.

As the authors argue, it would be intellectually dishonest to ignore hundreds of contradictory findings that cast severe doubt on a current theory and yet, that is precisely what postmodern archaeology is guilty of today.

There seems to be so much coming out by scientists not ground into the dogma of their prior academic standards, whether archaeology, geological etcetera. Although ridicule is still a barrier, many are delving deeper into disciplines of other, sharing, networking and laying out their findings alongside the statuesque. Funding is a huge factor of course, but little by little crakes are showing that cannot be ignored. Once the prior embedded puzzle pieces are removed; based either from original misinterpretation or camouflaged support of historical precedence, and tested, they just don’t fit anymore; the problem of course is that if you throw them away, there is no support as you alluded to not just in science but in other human fundamental areas too. These are big problems for people trying to maintain doctrines that are not maintainable under these new measures.

 

[Laura]

Cremo et al's collected evidence is pretty interesting as well, although I think Laura mentioned in another thread that his dates have to be taken with a grain of salt also because of the C-14 problem. 840,000 years ago is quite a stretch further than the 309,000 years ago when we are supposed to have arrived on the scene -- unless our apelike predecessors were quite sophisticated.

Yes, the dating thing is a real problem as far as I have been able to figure out from hundreds of sources and angles. At the same time, we don't know how many different "times" the Earth has been home to an advanced species. After all, with regular bombardment, or even the slower processes of deposition and/or erosion/decay, it's pretty hard to have a consistent, linear fossil record. When Burma Jones gets our timeline program up and running and accommodating really big dates, we can have some fun entering all the data from many sources and seeing how confused it gets! Of course, we may find that a pattern develops... which will also be interesting!

 

[Arctodus]

Oh my lord, that info regarding the penguins is _very_ interesting! Similar work has been done on tuataras IIRC. They have one of the fastest evolving genomes of any critters around today that we know of so far. Evolution in both genomes and phenotypes seems to be incredibly plastic. Good examples include up to six species of native Hawai'ian insects evolving exclusive dependency on bananas introduced by Polynesians. Or American apple flies evolving from basal hawthorne fly stock. Or those strange island lizards that developed herbivorous habits and cecal valves within 35 years. Or leopard-sized feral cats in Australia within just a couple of centuries.

Darwin's original basic concept of natural selection is still workable, within limits, evolution can happen at break-neck speed apparently. The whole field is going through a lot of change over time (pun definitely intended) Once taboo concepts like sympatric speciation, punctuated equilibrium, microbial lamarkism, hybrid speciation, etc. are just now getting much closer looks. The whole story is getting much more complex than was ever thought possible.

The redefining Man's Age article is a stumper. The quote that jumped out at me was this:"numerous cases of carved mammal bones presumably for decorative purposes dating to the Pliocene and Miocene (25 million years) eras." What mammal species are they? If they are typical of Miocene to Pliocene critters then yeah, it's a headscratcher. If they are typical of Middle to Late Pleistocene species, then they are in mis-dated deposits.

Looking at the comments of Shijing, Parallax and Mrs. Knight-Jadczyk regarding dating, I'm going to suggest that the fossil record is the "best" time-keeper we have for right now for Deep-Time. Not for accuracy of "time-frames" but simply because all other known dating methods are admittedly failures for Deep-Time. We can "see" transitions of flora and fauna from one depositional formation to another. Linear progressions are fairly obvious and no matter how intense an extinction event might be, some "archtype" critters and flora always manage to make it through and survive at least for sometime afterwards.

Mrs. Knight-Jadczyk's and the C's among others hypothesis that cataclysmic events can severely "magnetize" depositional formations is very intriguing. Given the embarrassing amounts of conflicting data and "circular reasoning" regarding most forms of dating, well...it is frustrating to say the least, aside from the fossil record, linear time on Earth seems to be an agreed upon "consensus" based on very questionable methods, which gets us nowhere.

 

[Laura]

I'm going to suggest that the fossil record is the "best" time-keeper we have for right now for Deep-Time. Not for accuracy of "time-frames" but simply because all other known dating methods are admittedly failures for Deep-Time. We can "see" transitions of flora and fauna from one depositional formation to another. Linear progressions are fairly obvious and no matter how intense an extinction event might be, some "archtype" critters and flora always manage to make it through and survive at least for sometime afterwards.

I'm going to agree with you here because I understand that you are saying pretty much the same thing I am saying: we can SEE a progression, we just don't know what dates to assign to it. That's why I have a problem with Cremo et al. They fall into the same trap of trying to assign dates though they go in a slightly different direction. It's sort of like the New Age types who theorize that Jesus married Mary Magdalene and get into a fight with the Christians. Problem is that they are both assuming that there is anything historical about the NT story. There MAY be, but what it is has to be extracted very carefully.

Mrs. Knight-Jadczyk's and the C's among others hypothesis that cataclysmic events can severely "magnetize" depositional formations is very intriguing. Given the embarrassing amounts of conflicting data and "circular reasoning" regarding most forms of dating, well...it is frustrating to say the least, aside from the fossil record, linear time on Earth seems to be an agreed upon "consensus" based on very questionable methods, which gets us nowhere.

Exactly. As I wrote in Secret History:

If we are going to investigate time, we will be confronted with the issue of dates, those markers of time, and of how these dates are established.

The most widely used method for determining the age of fossils is to date them by the “known age” of the rock strata in which they are found. At the same time, the most widely used method for determining the age of the rock strata is to date them by the “known age” of the fossils they contain. In this “circular dating” method, all ages are based on uniformitarian assumptions about the date and order in which fossilized plants and animals are believed to have evolved. Most people are surprised to learn that there is, in fact, no way to directly determine the age of any fossil or rock. The so called “absolute” methods of dating (radiometric methods) actually only measure the present ratios of radioactive isotopes and their decay products in suitable specimens - not their age. These measured ratios are then extrapolated to an “age” determination.

The problem with all radiometric “clocks” is that their accuracy critically depends on several starting assumptions, which are largely unknowable. To date a specimen by radiometric means, one must first know the starting amount of the parent isotope at the beginning of the specimen’s existence. Second, one must be certain that there were no daughter isotopes in the beginning. Third, one must be certain that neither parent nor daughter isotopes have ever been added or removed from the specimen. Fourth, one must be certain that the decay rate of parent isotope to daughter isotope has always been the same. That one or more of these assumptions are often invalid is obvious from the published radiometric “dates” (to say nothing of “rejected” dates) found in the literature.

One of the most obvious problems is that several samples from the same location often give widely divergent ages. Apollo moon samples, for example, were dated by both uranium-thorium-lead and potassium-argon methods, giving results, which varied from 2 million to 28 billion years. Lava flows from volcanoes on the north rim of the Grand Canyon (which erupted after its formation) show potassium-argon dates a billion years “older” than the most ancient basement rocks at the bottom of the canyon. Lava from underwater volcanoes near Hawaii (that are known to have erupted in 1801 AD) has been “dated” by the potassium-argon method with results varying from 160 million to nearly 3 billion years. It’s really no wonder that all of the laboratories that “date” rocks insist on knowing in advance the “evolutionary age“ of the strata from which the samples were taken -- this way, they know which dates to accept as “reasonable” and which to ignore.

More precisely, it is based on the assumption that nothing “really exceptional” happened in the meantime. What I mean by “really exceptional” is this: an event theoretically possible, but whose mechanism is not yet understood in terms of the established paradigms. To give an example: a crossing of two different universes. This is theoretically possible, taking into account modern physical theories, but it is too speculative to discuss its “probability” and possible consequences.

Could such an event change radioactive decay data? Could it change the values of some fundamental physical constants?

Yes, it could.

Is it possible that similar events have happened in the past? Yes, it is possible. How possible it is? We do not know. We do not know, in fact, what would be an exact meaning of the “crossing of two different universes”.

In addition to considering the idea of cataclysms that could have destroyed ancient civilizations more than once, there is another matter to consider in special relationship to radioactive decay: that ancient civilizations may have destroyed themselves with nuclear war.

Radiocarbon dates for Pleistocene remains in northeastern North America, according to scientists Richard Firestone of Lawrence Berkeley National Laboratory, and William Topping, are younger as much as 10,000 years younger than for those in the western part of the country. Dating by other methods like thermo-luminescence (TL), geoarchaeology, and sedimentation suggests that many radiocarbon dates are grossly in error. For example, materials from the Gainey Paleoindian site in Michigan, radiocarbon dated at 2880 yr BC, are given an age by TL dating of 12,400 BC. It seems that there are so many anomalies reported in the upper US and in Canada of this type, that they cannot be explained by ancient aberrations in the atmosphere or other radiocarbon reservoirs, or by contamination of data samples (a common source of error in radiocarbon dating). Assuming correct methods of radiocarbon dating are used, organic remains associated with an artifact will give a radiocarbon age younger than they actually are only if they contain an artificially high radiocarbon keel.

Our research indicates that the entire Great Lakes region (and beyond) was subjected to particle bombardment and a catastrophic nuclear irradiation that produced secondary thermal neutrons from cosmic ray interactions. The neutrons produced unusually large quantities of Pu239 and substantially altered the natural uranium abundance ratios in artifacts and in other exposed materials including cherts , sediments, and the entire landscape. These neutrons necessarily transmuted residual nitrogen in the dated charcoals to radiocarbon, thus explaining anomalous dates. […]

The C14 level in the fossil record would reset to a higher value. The excess global radiocarbon would then decay with a half-life of 5730 years, which should be seen in the radiocarbon analysis of varied systems. […]

Sharp increases in C14 are apparent in the marine data at 4,000, 32,000-34,000, and 12,500 BC. These increases are coincident with geomagnetic excursions. […]

The enormous energy released by the catastrophe at 12,500 BC could have heated the atmosphere to over 1000 C over Michigan, and the neutron flux at more northern locations would have melted considerable glacial ice. Radiation effects on plants and animals exposed to the cosmic rays would have been lethal, comparable to being irradiated in a 5 megawatt reactor more than 100 seconds.

The overall pattern of the catastrophe matches the pattern of mass extinction before Holocene times. The Western Hemisphere was more affected than the Eastern, North America more than South America, and eastern North America more than western North America. Extinction in the Great lakes area was more rapid and pronounced than elsewhere. Larger animals were more affected than smaller ones, a pattern that conforms to the expectation that radiation exposure affects large bodies more than smaller ones. (Firestone, Richard B., Topping, William, Terrestrial Evidence of a Nuclear Catastrophe in Paleoindian Times, dissertation research, 1990-2001.)

The evidence that Firestone and Topping discovered is puzzling for a lot of reasons. But, the fact is, there are reports of similar evidence from such widely spread regions as India, Ireland, Scotland, France, and Turkey; ancient cities whose brick and stone walls have literally been vitrified, that is, fused together like glass. There is also evidence of vitrification of stone forts and cities. It seems that the only explanation for such anomalies is either an atomic blast or something that could produce similar effects, which we will get to soon enough.

But still, we ought not to give up. My idea is that we should just continue to gather data and allow for the various processes that may (probably did) occur on earth at various points of apparent discontinuity and just try to see where the data leads us. The Cs are all fine and good for inspiration, but nothing takes the place of some hard work on collecting data and assembling it into a usable structure. We just have to leave off the dates for right now.

There is one thing that I think we can pretty firmly date: the eruption of Thera.

Thera volcano catastrophe dated to 1613 BCE

Archaeo News
Sat, 06 Dec 2008

Two olive branches buried by a Minoan-era eruption of the volcano on the island of Thera (modern-day Santorini, Greece) have enabled precise radiocarbon dating of the catastrophe to 1613 BCE, with an error margin of plus or minus 10 years, according to two researchers who presented conclusions of their previously published research during an event at the Danish Archaeological Institute of Athens.

Speaking at an event entitled 'The Enigma of Dating the Minoan Eruption - Data from Santorini and Egypt', the study's authors, Dr. Walter Friedrich of the Danish University of Aarhus and Dr. Walter Kutschera of the Austrian University of Vienna, said data left by the branch of an olive tree with 72 annular growth rings was used for dating via the radiocarbon method, while a second olive branch - found just nine metres away from the first - was unearthed in July 2007 and has not yet been analysed. The researchers said both olive tree branches were found near a Bronze Age man-made wall, giving the impression that they were part of an olive grove situated near a settlement very close to the edge of Santorini's current world-famous Caldera. The two trees were found standing when unearthed, and apparently had been covered by the Theran pumice immediately after the volcano's eruption.

According to the two scientists, other radiocarbon testing from archaeological locations on Santorini and the surrounding islands, as well as at Tel el-Dab'a in the Nile delta in Egypt, corroborate the dating based on the olive tree. On the other hand, as the two researchers pointed out, archaeological evidence linked with the Historical Dating of Ancient Egypt indicate that the Thera eruption must have occurred after the start of the New Kingdom in Egypt in 1530 BCE. The two researchers said their find (olive tree) represents a serious contradiction between the results of the scientific method (radiocarbon dating) and scholarly work in the humanities (history-archaeology), with both sides holding strong arguments to support their conclusions. The radiocarbon dating places the cataclysmic eruption, blamed for heralding the end to the Minoan civilisation, a century earlier than previous scientific finds.

I think that if the archaeologists could just give up their attachment to their dates and go with this "hook" on which to hang the whole ME chronology, things might begin to straighten out. After all, their dates are based pretty much on the Bible which was the foundation of the "science of archaeology." They all assumed that the Bible was history and it is NOT!

 

[shijing]

I'm going to agree with you here because I understand that you are saying pretty much the same thing I am saying: we can SEE a progression, we just don't know what dates to assign to it. That's why I have a problem with Cremo et al. They fall into the same trap of trying to assign dates though they go in a slightly different direction...

But still, we ought not to give up. My idea is that we should just continue to gather data and allow for the various processes that may (probably did) occur on earth at various points of apparent discontinuity and just try to see where the data leads us. The Cs are all fine and good for inspiration, but nothing takes the place of some hard work on collecting data and assembling it into a usable structure. We just have to leave off the dates for right now.

You're talking about building a relative chronology, and I agree its the best way to go about things. I run into this problem a lot in my own field, where it is often fairly straightforward to place events in sequence based on available data, but much more difficult to assign specific dates to any of those events. However, knowing the relative sequence is the most important thing, because it allows you to see which event X preceded which other event Y, thereby establishing causality, which allows you to figure out why things happened and to reconstruct events from the bottom-up, going backwards in time (and sometimes filling in the more specific gaps between time A and time B, once a data feedback loop is established between those two points). Assigning absolute dates then just becomes icing on the cake if you discover a reliable means to do so.

 

[Brenda86]

Quote from Laura:

They all assumed that the Bible was history and it is NOT!

It never ceases to amaze me how even with all the evidence backing this up, how extremely educated and otherwise logically thinking people can continue to believe that it is indeed history.

 

[Juba]

Seems like penguins are not only species dislocated in time by GD techniques, here are some interesting quotes from: Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations Under a Range of Demographic Models written by: MURRAY P. COX

quote:

-The ρ statistic is commonly used to infer chronological dates for molecular lineages, especially from mitochondrial DNA sequences obtained in anthropological contexts. Since this approachwas described 12 years ago, it has been applied to estimate molecular dates in more than 200 studies, including some published in top-tier journals. However, this method has not been well evaluated, and the accuracy of dates obtained from the ρ statistic remains unknown, especially for genetic data collected from populations with complex demographic histories. Here, molecular dates inferred from ρ are compared against coalescent expectations from a range of demographic models. This exercise reveals considerable inaccuracy.

-Molecular dates based on ρ have a slight downward bias with large asymmetric variance and commonly exhibit substantial type I error rates, where the true age of a lineage falls outside the 95% confidence bounds derived from the variance of ρ.


-Molecular Dating with the Rho Statistic / 337 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 of the ancestral node in real chronological time. Confidence intervals on this date can be derived from the expected variance of . This dating approach is relatively simple, but its accuracy remains unknown. However, it seems unlikely that the method is routinely accurate, particularly given the variance of genetic data sets generated under even the simplest demographic models. It is therefore reasonable to question the accuracy of molecular dates inferred by applying this method to empirical data sets with more complex demographic histories. Here, I use coalescent modeling to determine the accuracy of molecular dates estimated from the statistic. First, I examine the bias and variance of point estimates of dates obtained for a simple constant-size population. Next, I consider different methods of constructing confidence intervals and determine their error rates. Finally, I investigate the accuracy of molecular dates obtained under a range of more complex demographic models (e.g., those including population growth, bottlenecks, and structure). I conclude that genetic dates inferred from the statistic are often slightly downward biased with large asymmetric variance and that they commonly exhibit substantial type I error rates, where the true date for more than 5% of data sets lies outside the 95% confidence bounds estimated from the variance of . Furthermore, the widely held perception that the accuracy of dating is independent of demography is false; type I error rates commonly depend on the demographic history of the study population.

-The known coalescent TMRCA is compared with the -based estimator of TMRCA and its confidence intervals. Because all other simulation parameters are known absolutely, any bias, variance, or error in the estimated TMRCA necessarily reflects inaccuracy associated entirely with the -based dating method.

-Molecular Dating with the Rho Statistic / 341 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 without error to be 9,300 years. Observe that an average of 2.1 polymorphisms (standard deviation of 0.92 polymorphism) occurs along each unique lineage l from the MRCA (the average is weighted by the number of individuals sampled with each lineage). Given a sequence length of 500 bp and a mutation rate of 1.8 x 10 -7/bp/yr, the expectation is to observe 1 mutation every 11,111 years; this is the mutation rate scalar described by Eq. (4). The product of the statistic and the mutation rate scalar estimates the TMRCA of this data set at 23,300 years (95% confidence interval [3,250-43,400]). Here, the TMRCA estimated from is more than twice as large as the true TMRCA, and although the 95% confidence interval inferred from the variance of incorporates the true age (i.e., 9,300 years), the breadth of these confidence bounds is considerable. As will be seen, this is a relatively positive outcome from inferring molecular dates with the statistic. In the following sections, I examine several key characteristics of -based molecular dating, including the accuracy of TMRCA estimates from a single panmictic population of constant …

PS: About RHO Spearman statistic: These responses are subsequently converted to numbers, where A=1, B=2, C=3, D=4, and E=5. Such data do not meet the requirements of the Pearson r because they are not interval. To perform a correlation on data that are not interval, perform the Spearman rho statistic, which requires that data in each variable must be at least ordinal.

PPS: About coalescent expectations;

-
* Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models.
Hum Biol Mar 25, 2009
... demographic histories. Here, molecular dates inferred from rho are compared against coalescent expectations from a range of demographic models. This exercise reveals considerable inaccuracy.

-Am J Hum Genet May 15, 2003
... intervals in the matrilineal and patrilineal genealogies, which was stronger in matrilines and thus contributes to their faster evolutionary rate. These findings may have implications for coalescent date estimates based on mtDNA and Y chromosomes.

-Integrating coalescent and ecological niche modeling in comparative phylogeography.
Evolution Jun 04, 2007
... . Paleodistributional models introduce a much-needed spatial-geographic perspective to statistical phylogeography. In conjunction with coalescent models of population genetic structure, they have the potential to improve our understanding of the factors

-DNA sequence variation in a non-coding region of low recombination on the human X chromoso
Nat Genet May 25, 1999
... typically determined. It is currently unclear how some forms of analysis (such as the coalescent) should be applied to such data. Furthermore, the lack of recombination ... 535,000+/-119,000 years. We expect this type of nuclear locus to provide more answers ..

-

In other words, if the data are ordinal, or if they are interval but not normally distributed, then employ the Spearman rho statistic. If your data are both interval and normally distributed, do not use Spearman rho as it is a weak statistic that should be employed only if absolutely necessary.

So, I guess I'll wait for REAL chronological dates for human molecular lineages or simply continue to read and explore C's transcripts.