You’d think that there would be little left to figure out about Mann’s PC methods. I’ve been re-examining the PC1 in Mann and Jones  and Jones and Mann  for reasons that I’ll explain further in my next post. The data is at WDCP here but I wasn’t able to replicate this result and had basically given up temporarily. Since I don’t like loose ends, it’s irritated me. Out of the blue, I figured out what he did. The solution was splicing of Mannian proportions.
Let’s review the clues. We know that MBH98 and MBH99 uses a screwy PC methodology. Mann and Jones  say in addition only the following:
western North American tree-ring temperature reconstruction, (warm season temperature [Mann et al., 1999]; we employ an extension of the first principal component of the western North American tree-ring data based on 6 ultra-long lived, temperature-sensitive Western North American tree ring records available back to AD 200″¢’¬?the resulting series is virtually indistinguishable from the corresponding Principal Component (PC) series used by Mann et al.,  based on 27 available chronologies during the AD 1000–1980 overlap interval).
I was able to replicate the selection of 6 sites pretty easily. I’ve done a collation of details such as start date, type etc. for the ITRDB North American tree ring data base which I use all the time (this is inherent in the WDCP functions but unfortunately not available as a data frame). Using these start dates, requiring a start prior to 201, for series with the ITRDB ids from MBH98, I located exactly 6 sites. Five of the 6 were (surprise, surprise) bristlecones; the 6th was a New Mexico site of Grissino-Mayer, used in precipitation reconstructions. One of the sites is our old favorite, Sheep Mountain.
When I did a mannomatic PC calculation on these 6 sites, the eigenvector weight of Sheep Mountain (coefficient^2) is over 80% – so it wears the pants in the PC1. There is some additional information on the PC1 in the caption to Figure 4 of Jones and Mann  which says:
Local and regional proxy temperature reconstructions by continent. Source references for all series are given in Table 1. Each series has been normalized over the period 1751–1950 and then smoothed with a 50-year Gaussian filter. For the decadally resolved data the normalization period is the 20 decades from 1750 to 1949, smoothed using a 5-decade filter.
Table 1 merely cites MBH98 as authority (not Mann and Jones, 2003), but claims an annual correlation of 0.20 to gridcell temperature and 0.56 to decadally smoothed temperature. It states that the corresponding instrumental data is either for the overlying 5 degree by 5 degree grid box (for single-site proxies) or averages of several boxes (for regional or multiproxy series). There is a comment in passing about CO2 fertilization in Jones and Mann, 2004:
During the most recent decades, there is evidence that the response of tree ring indicators to climate has changed, particularly at higher latitudes and more so for density than ring width measurements [Briffa et al., 1998a]. One suggested source for this behavior is “Å”ÅCO2 fertilization,” the potential enhancement of tree growth at higher ambient CO2 concentrations. Though it is extremely difficult to establish this existence of this effect [Wigley et al., 1988], there is evidence that it may increase annual ring widths in high-elevation drought-stressed trees [Graybill and Idso, 1993]. Recent work making use of climate reconstructions from such trees has typically sought to remove such influences prior to use in climate reconstruction [Mann et al., 1999; Mann and Jones, 2003].
Now as noted above, Mann and Jones 2003 does not refer to any "adjustment", but MBH99 has a ridiculous adjustment which imputes CO2 fertilization in the 19th century and negative fertilization in the 20th century. There are "fixed" PC1s and the calculation is inelegant but can be decoded from information at the UVA site. The earliest directory containing "fixed" data is AD1000.
I noticed that the early portion of the plot for the emulated PC1 (using the mannomatic method) looked a lot like the archived version. In fact, it proved to have a correlation of >0.9999 for selected early intervals. With some experimentation, this value extended for the period from 200 to 1699 – so the archived version was definitely a re-scaled version of the mannomatic PC1 up to 1700 (but the relationship broke down afterwards.) The "fixing" of the AD1000 PC1 takes place after 1700 – so on a hunch I tested the correlation between the AD1000 "fixed" PC1 and the archived AD200 PC1 – bingo, there was a correlation of >0.9999. So the latter portion was a re-scaled version of the AD1000 "fixed" PC1, which was spliced with the AD200 mannomatic PC1.
Thus there were two successive "adjustments": first the AD1000 PC1 was coerced to have a low-frequency shape like the Jacoby NH composite (this is alluded to in MBH99); then this adjusted PC1 for the AD1000 period is spliced with the AD200 PC1. Remember the hyper-ventilating at http://www.davidappell.com about splicing PC series (which Rutherford and perhaps others had done in the file pcproxy.txt – the file originally provided to us. Here’s another example.