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The Ketchum Report (Part 3)

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southernyahoo

Well we got started when you maligned the idea that they are human, which is a descriptor I'm sure we would "have" to use if the DNA IS modern human in the mitochondria, societal baggage or not. Redefining "human" would be bound to happen and appaul many I'm sure when we consider they live in the wild like an animal yet would have "human rights" and abide by "no" laws. It would create a huge fissure in our legal system and divide people on what is right and wrong in dealing with them.

That my freind, is the major road block of recognition and acceptance, and we can't really even touch on the religous implications of such an outcome.

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Guest DWA

Yes, but I'm not "maligning" anything.  That implies malice.  I am neutral on this subject...except as to the evidence.  My views reflect my take on that, and only on that.

 

When Alley went over the possibilities in Raincoast Sasquatch, I just knew he was gonna blow a tire on "maybe they're genus Homo."  He didn't; he gave an intriguing and fascinating take.  But I'd need to see more evidence than I have to bet that.

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southernyahoo

^My bad, I guess I sensed some hostility in this quote below........

 

The best thing that will come from killing this Ketchum noise is another nail in the coffin of "they're human."

 

LOL silly me. :lol:

 

BTW, I've talked to Alley, and he is certainly open to them being genus homo, though he also seemed a little surprised by these results.

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Has anyone else been able to read the documents that were posted online?

 

https://docs.google.com/file/d/1DwVFfFOS6iX9yNQrxcSBRqRwQRn3Bkoi_3nnFDtR7-eDUkx-HOP-NjMYbG8M/edit?pli=1

https://docs.google.com/file/d/1UpuWi01e6aFefwbZtnlLVVB3q6ERADEKrdN2KFnAGaPK9mqTTrDqrjKLkm2F/edit?pli=1

 

The first is claimed to be Melba's responses to Nature's request for changes. The second is supposed to be a letter from Melba to Nature.

 

I can't read them because my laptop won't open them.

I downloaded from RL's and thinking about doing so, I used the print option and saved as PDF.....

...although my recent tutorial on genetics will not suffice I am sure.

 Interesting timing to this release.

 

RL also made comment of the Max Planck announcement to impress all Anthropology....wouldn't that be nice if bigfoot..

 

But I don't think so, I think they will show additional passes on the Neandertal genome, and maybe Denisova ...  but what new might arise from that?  Better draft genomes...  maybe more clearly interbreeding shown...?

 

Could there be an erectus fossil yielding DNA?  Florensis was degraded....

 

Or could it be BF and RL's/Dyer famed hidden body...

 

geesh.. I now get after hanging around a few years..this kind of rumor undercurrent and hope/disappointment is the norm!

Edited by apehuman

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Guest DWA

^My bad, I guess I sensed some hostility in this quote below........

 

 

LOL silly me. :lol:

 

BTW, I've talked to Alley, and he is certainly open to them being genus homo, though he also seemed a little surprised by these results.

The hostility was to the Ketchum noise, by which I stand.

 

When a scientist acts like she has, well, the results can be anticipated.  If one isn't acting like a scientist in the prep and the presentation, why expect impeccable results?

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Has anyone else been able to read the documents that were posted online?

 

https://docs.google.com/file/d/1DwVFfFOS6iX9yNQrxcSBRqRwQRn3Bkoi_3nnFDtR7-eDUkx-HOP-NjMYbG8M/edit?pli=1

https://docs.google.com/file/d/1UpuWi01e6aFefwbZtnlLVVB3q6ERADEKrdN2KFnAGaPK9mqTTrDqrjKLkm2F/edit?pli=1

 

The first is claimed to be Melba's responses to Nature's request for changes. The second is supposed to be a letter from Melba to Nature.

 

I can't read them because my laptop won't open them.

 

I have converted one to Google docs and copied it. Attempting a paste here so you and anyone else having trouble can see it. It appears to have worked but the spacing might be off: 

 

 

Author Responses to Referees

 

Referee #1 (Remarks to the Author):

I must state at the outset that I am not a geneticist, and hence not fully qualified to evaluate the DNA data in proper critical fashion. Bottom line: there is obviously the backbone here of a paper that includes a lot of interesting data, but it needs a lot of work before it can be accepted.

1. My main advice (discussed further below): include better graphics (especially a similarity tree/distance tree/phylogram/cladogram of some sort).  

Authors’ Response: We have added 9 phylogenetic trees and added more data in the form of whole genome sequencing.

 

2. Remove the problematic conclusions on taxonomic status and the unnecessary section on recent hominin discoveries, and tidy up the nomenclature and wording.

-- Discussion of fossil species is probably irrelevant

The manuscript opens with a section on how recently discovered fossil hominins have changed our views on the hominin diversity of the recent past. While it seems logical to mention these taxa in passing at least somewhere in the manuscript, I think it's a bad idea to start the article off with a discussion of these forms - is this really the area of investigation that most requires review when writing about the possible existence of sasquatch? I would say no.  The authors are meant to be addressing the possible existence and identity of an extant population, not adding to the roster of fossil forms. In other words, the discussion of Neanderthals, Denisovans and so on seems like unnecessary padding.  There are some basic mistakes concerning terminology and the use of binomials (e.g., the name _Homo floresiensis_ is incorrectly written with capital first letter on the species name). Neanderthals do not have the name they do "because of their skeletal morphology" (rather, they are distinguished by their skeletal morphology).

Authors’Response:  We removed the taxonomic recommendation.  Additionally we removed the recent hominin discoveries (Neanderthal and Denisovan).

 

3. It would seem far more appropriate so far as I can see to begin with a discussion of the controversy surrounding the purported existence of 'mystery hominoids', and to perhaps allude to some of the other technical studies that have claimed to find evidence for the existence of these alleged creatures.

Authors’ Response:  The discussion of the controversy surrounding the existence of these hominins was moved to the introduction and expounded on, including photos and video. References were added from other scientific papers and books published addressing the existence or the discussion of the existence of these hominins.

4.-- Demonstrate with better clarity what the DNA samples represent

It is stated in the discussion of the collected DNA samples that those "not consistent with _Homo sapiens sapiens_" were then evaluated further. I feel the authors must elaborate on what it was that made it clear that the samples were not part of _H. s. sapiens_ - the normal graphic way of representing this is, of course, a gene tree, distance tree or cladogram of some sort. If the authors are saying that the samples are from a hominid and hominin, but come from a taxon outside of _H. s. sapiens_, they need to state it more clearly and provide better evidence and clearer graphics. Any diagram should also make it clear that other mammals (a useful list is included in the manuscript) were definitely out-groups relative to the group that includes the 'mystery' samples and those of definite hominins.

Authors’Response:  We clarified and removed the verbiage stating "not consistent with _Homo sapiens sapiens_".  We have added 6 mitochondrial phylogenetic trees which clearly show the samples had modern human maternal origins and were generated via conventional sequencing as well as phylogenetic trees extracted from next generation whole genome sequences.  We provide more evidence by sequencing 3 whole genomes at the University of Texas core lab and using a  subsample of extracted reads.  The reads were assembled to create a consensus sequence using the human chromosome 11 as a reference.  These concatemers (supercontigs) were used to find sequence homologs and generate 3 phylogenetic trees, one for each whole genome sequenced.   

5. -- Terminology seems odd and needs changing

The terminology used throughout this manuscript, and the conclusions the authors reach, seem inappropriate in view of the evidence. Indeed, the title tells us that evidence for a 'new species' is presented, yet the authors actually end up naming a new 'subspecies'. I am definitely of the opinion that the naming of a new taxon seems inappropriate at this stage (it is likely to be about as accepted as Meldrum's suggested ichnotaxonomic name _Anthropoidipes ameriborealis_), and I would also add that the chosen name ('_Homo sapiens feralis_') is odd and highly problematic (use google to see what I mean). It is stated throughout the ms that the animal is of hybrid origin. If this is so, it is highly debatable as to whether or not taxonomic novelty is warranted.

Authors’Response:  We have re-written and re-arranged the manuscript to use better terminology and also have removed any taxonomic references other than to call the hominins Sasquatch.

 6. I would like to know exactly what is meant by those statements noting that the "paternal lineage [is] completely unknown", as the authors seems to be introducing a new layer of mystery to their conclusions. It seems radical enough that they are positing a hybrid origin for this putative animal, but are they also invoking the existence of an additional animal that was involved in the proposed hybridisation event? This all seems very peculiar and I am not convinced that the evidence presented in this manuscript explains it adequately.

Authors’Response:  By sequencing 3 whole genomes that failed to align with any animal or hominin found in NCBI, there is no other conclusion other than that the paternal nuclear DNA origins are unknown.  Previous data suggested that novel sequences and high failure rate were found in the nuclear DNA sequencing and STR testing., The addition of the three genomes further supports our initial findings.  The nuDNA and  mtDNA origins of the Sasquatch are discordant, with mtDNA indicating human maternal lineage. Analysis of the 3 next generation whole genome sequences and analysis of preliminary phylogeny trees from the Sasquatch indicate that these individuals possesses an anomalous mosaic pattern of nuclear DNA comprising sequences that are distantly related to primates interspersed with sequences that are closely homologous to humans.

 

7. I would also suggest that the phrase "unknown morphology of the hair" is inappropriate: rather, the authors are reporting a morphology that is novel.

Authors’ Response:  We changed the phrase "unknown morphology of the hair" to “microscopic morphology of hairs classified as “novel†and “novel hairsâ€.

8. All in all, this manuscript seems to report the discovery of a novel North American hominin lineage as determined by DNA analysis (so far as I can tell, the substantial discussion of that data is appropriate and does consider most relevant factors/avenues of investigation). This is, obviously, potentially, a significant, Nature-worthy discovery. But it is marred by poor choice of presentation (that is, the absence of a tree that immediately conveys the position of the samples to those of other taxa/populations), unnecessary discussion of fossil forms, and inappropriate, confusing and rather naive proposals concerning nomenclature and the alleged hybrid origin of the alleged animal. I would definitely like to see this manuscript 'salvaged', but it would need a thorough revision and re-organisation. I wish the authors the best of luck in their continuing efforts.

Authors’ Response:  We re-organized and revised the manuscript and added extra data to support our original findings.

 

Referee #2 (Remarks to the Author):

The authors analyse some biology samples (mainly hairs) putatively belonging to the Big Foot; they analyse the hair microscopica structre, the mtDNA, forensic STRs markers and some few nuclear genes -including the MC1R- and conclude the results indicate the existence of a previously unknown human species, which they call Homo sapiens feralis. I am not going to go into the specific details of the results, which are quite confusing and methodologically debatable, but will explain what the average molecular biologists would do in two different scenarios related to the problem presented in this work.

1. Identify a biological sample of unknown specific origin, say, hairs, or coprolites or blood stains. This approach is widely used in zoology, for instance, to distinguish between wolf and dog after an attack to a sheep herd. Usually the people uses universal primers to amplify a diagnostic DNA fragment that could help in the identification of numerous species. 16S is probably the most widely used, although in specific situations and for trying to find out the precise match, you may want to design additional tests on cytb, nuclear SNPs, complete mtDNA, etc. This has not been done here; the use of human primers will amplify human mtDNA, as has been the case. Moreover, the fragmentary mtDNA data does not support any unknown hominin lineage, because the haplotype/haplogroup attribution fits well in what is already known of the modern human mtDNA phylogeny.

Authors’Response:  The evidence samples were screened with not only published cytochrome b primers utilized for species identification but also THR/DHL which are universal mammalian primers in the literature utilized across HV1 for species identification.  This is stated in the manuscript however, we have made it more prominent.  We also had previously sequenced a number of whole mitochondrial genomes which are in the manuscript.  We have increased that number.  The initial mtDNA screening of the samples with the universal primers yielding only human results. These findings are consistent with previous attempts by other labs and scientists to validate the existence of Sasquatch through mtDNA which we have documented in the Discussion.  There was no DNA of any other species in the mtDNA in any of the samples utilized in this study. The whole mitochondrial genomes were consistent with modern human as were the samples that yielded enough mitochondrial sequence to assign a haplotype but not a whole mtDNA genome.  Even the samples with very little DNA (not enough to achieve a haplotype) were screened with a short HV2 sequence and gave only human sequence. This mtDNA alone did not support an unknown hominin, however the same extractions, when sequenced on various nuclear loci and amplified with PowerPlex 16, yielded unexpected and aberrant  results with some loci yielding normal human sequence along with novel sequences not found in genetic depositories.    To further support our findings, we have sequenced 3 next generation whole genomes from which 3 mitochondrial DNA sequences were extracted and were homologous with human and the previous sequencing.  The chromosomal sequences were discordant and novel, supporting the original findings.

2) Another scenario. We want to prove that the specimen we are studying is an undescribed, new species. Of course the definition of what a species would look like genetically is a tricky question (see for instance, the Denisovans), but you would be expected to generate a huge amount of genomic data (if possible, the complete genome), construct phylogenetic trees and show that your specimen represents a deep, undescribed clade in the current phylogeny. Even so, some might argue that genetic divergence is not equivalent to species difference, but at least you would have a good point to support your claims. This has not been done here, and the analysis of three random nuclear genes cannot be used for the purpose of defining a new species.

In short, the conclusions are not supported by the methodology. I would suggest the authors to generate complete mtDNA genomes and, if possible, suficient nuclear data, even from shotgun approaches, and build phylogenetic trees with all possible mammal mtDNA genomes and nuclear data available at genbank.

Authors’ Response:  We added more data to the manuscript by sequencing 3 whole genomes using next generation sequencing.  Previous data suggested that novel sequences and high failure rate were found in the nuclear DNA sequencing and STR testing. The addition of the three genomes further supports our initial findings.  The nuDNA and  mtDNA origins of the Sasquatch are still discordant, with mtDNA indicating human maternal lineage. Analysis of the 3 next generation whole genome sequences and analysis of preliminary phylogeny trees from the Sasquatch indicate that these individuals possesses an anomalous mosaic pattern of nuclear DNA comprising sequences that are distantly related to primates interspersed with sequences that are closely homologous to humans.

 

Referee #3

(Remarks to the Author) I believe that among the most important abilities defining a real scientist is his/hers ability to stay open-minded and accept that the world may be radically different from common believes as long as such radical claims are supported by sufficient hard scientific evidence. Such a radical claim is presented by Ketchum et al. that basically propose the existence of new contemporary sub-species of homo in North America termed Homo sapiens feralis. The claim is based on morphological and DNA based analyses of samples such as hair and bark shavings, tissue, toenail, saliva, and blood samples taken by various people in areas where unusual bipedal hominin like creature has been visually observed. Based on these analyses the authors claim to have found evidence of a new contemporary hominin with unique hair, strange, nuDNA, and human mtDNA. An exceptional claim such as this demands for exceptional convincing evidence - something the authors do not have:

1. First the data does not make logical sense. Mitochondrial DNA genomes being identical to that of contemporary humans can only be explained be relative recent interbreeding between this new hominin and woman of Caucasian descent. Did such interbreeding go back many thousands of years one will expect differences to modern mtDNA genomes. The mtDNA results are hardly explainable unless one believe that American woman of Caucasian descent (within the last 200-300 years as its America) runs around in the forest having sex with a undiscovered hominin and leavening the baby to their care take of the new hominin (as the rest of us have not heard about such hybrid babies yet the baby must be send of). It is also sticking that the entire mtDNA lineages of this new hominin is poorly human. One would expect at least some mtDNA genomes coming out as being accordance with this being a new hominin or if nothing els some of the mtDNA being Native American (everything being equal they have been in America more than 10,00 0 years).

Authors’ Response:  We now have two samples that did yield American Indian haplotypes.  These were late arriving samples and were added to the manuscript.  As far as when this species arrived in the United States, we do not know, however due to H haplotypes in their mitochondrial DNA, the age of these hominins is less than 15,000 years.  However, they could have arrived in the United States before Native American peoples according to the Solutrean Theory now added as a reference in this manuscript.  As far as the mitochondrial DNA being homologous to human, we used next generation whole genome sequencing on three samples.  The mitochondrial DNA sequences were extracted from the genomes and all three were consistent with the same human mtDNA sequence previously sequenced in the beginning of our study.  The nuDNA however, was a mosaic of human sequence interspersed with novel sequence related to primate lineage.  This supports the previous findings reported in the original manuscript.

 

2. Secondly, PCR based methods and methods used for SNP detection by the authors are known to be highly unreliable when applied to minor amounts of degraded DNA (I know that personally for the SNP detection approach and simple PCR). This is especially the case for nuDNA templates that are more prone to be affected by damage than those of mtDNA (due to copy number differences). In fact copy number differences can very well explain the DNA findings i.e. the specimens are human in origin, why the authors amplify mtDNA genomes marching contemporary Caucasians. The nuDNA , however, is too poor quality for amplifying the attempted sequence length and creating PCR artifacts. It makes good sense even for the hair sharft samples that by nature has degraded DNA (even when taken "fresh") . I am sorry but this appears to be a much more straightforward scenario than having a previously undetected (by science) hominin sub-species running around in the forest mating with Caucasian woman. I am by no means convinced that this has anything to do with a new hominin subspecies. To make a compelling case I need seeing mtDNA genomes and large numbers of nuDNA sequences that points in direction of a new hominin species i.e. ape or human like without being identical to know species.

Authors’ Response:  We have now included Figures 7 and 13 that show the quality of the DNA on yield gels.  There was little to no smearing and the DNA was pristine.  This supports the fact that the DNA was not degraded enough to mar the results.  We sequenced 30 mitochondrial whole and partial genomes and they were all homologous with modern human mtDNA.  We also sequenced several nuclear loci from the same extractions which encompassed a number of long sequences up to 900 bases.  It is difficult to amplify and sequence long amplicons with degraded DNA.  In order to ascertain if the novel nuclear DNA was an anomaly, we used next generation sequencing to generate 3 whole genomes to determine if the nuclear DNA was indeed novel.  If the DNA was badly degraded, the sequencing of whole genomes would have been impossible.  The 3 extractions utilized for next generation whole genome sequencing passed all quality controls in our laboratory and the university core laboratory prior to sequencing. The libraries generated from these samples also passed stringent quality control measures in the core laboratory prior to the next generation sequencing.  If the libraries had not passed QC, the sequencing would not have been performed. We have furnished 9 phylogenetic trees (mitochondrial and nuclear) to support the results of this study.  

 

3. I'm not an expert on hair morphology but I expect that identification mistakes are made.

Authors’ Response:  The hair expert that examined the hair is a forensic trace evidence supervisor in a large forensic laboratory.  He performs hair analysis and testifies about his findings in court on a daily basis.  He also testifies concerning and examines hair from many species of animals as well as human.  Furthermore, he had a wide collection of animal hair standards with which to compare these hair samples utilized in this manuscript.

 

Referee #4 (Remarks to the Author):

The authors seek to identify the species of 130 unknown, though purportedly hominin, hair and tissue samples. The samples are subjected to multiple forensic and genetic tests, including hair analysis, mitochondrial and nuclear genome sequencing and electron microscopy. They postulate that, while the mitochondrial genomes of all tested samples are conclusively human, discrepancies in Y-chromosome STR and amelogenin amplification, lack of sequence homology to known species, as well as structural abnormalities in DNA viewed by electron microscopy are indicative of an unusual hominin source. They identify this source as a new species, which they call Homo sapiens feralis.

Extraordinary claims require extraordinary evidence. At no point do the authors provide adequate evidence to support their outrageous claims. The paper suffers from a myriad of faults, some of the most egregious being:

1. Results are not documented in any adequate detail. For example, the DNA sequences determined are not given, rendering any coherent understanding of the results impossible.

Authors’ Response:  Sequences not shown in mutation reports have been added to the Supplemental Data. Mutation reports are now added to the manuscript in the Supplemental Data allowing transparency of sequences previously reported as well as new sequencing that has been added.

 

2. Failures in tests such as SNP analysis, amplification and electrophoresis are taken as evidence for differentiation, when they are likely explained by DNA degradation or contamination. In one instance the authors attempt to replicate DNA degradation by leaving a blood sample at room temperature for 4 days and using the sample as a positive control in further testing. They fail to assess the extent of degradation quantitatively, making this positive control uninformative.

Authors’ Response:  We have added Figure 13 to show the level of degradation of the human control sample in comparison with some of the Sasquatch samples in the study.  We have added 3 whole genomes that were successfully sequenced using next generation sequencing technology.  These genomes supported our previous data and were novel.  Furthermore, we have added photos of the raw extracted DNA on agarose to support the quality of the DNA.  

 

3. When an unknown DNA sequence is amplified from a sample this is taken as evidence that it comes from the purported unknown hominin when in fact mispriming from DNA of an unknown microorganism is a much more plausible scenario.

Authors’Response:  We used next generation sequencing to sequence three unique whole genomes.  The findings from these genomes support our previous findings.  These samples were high quality and yielded outstanding genomes.  The quality control prior to sequencing ruled out any large degree of bacterial contamination.  We also provided new Figures 7, 8 and 13 to address any levels of degradation and contamination. Figure 13 and 8 as well as the histopathology report on Sample 26 which was added intentionally to show that that sample 26, which was one of the whole genomes sequenced, was neither degraded nor had a high concentration of bacteria.   Figure 7 was a yield gel showing some of the DNA utilized in this study.  Note that the samples are not smeared.

 

4. Genetic differentiation based on electron microscopy is improbable. On this scale, one cannot distinguish the differences between any two species. The observed structural differences, if legitimate, are at best indicative of DNA damage.

Authors’Response:   The electron microscopy was not intended to provide species identification but was included as supporting evidence for the unusual behavior of the amplified DNA.  We have further addressed this in the revised manuscript.

 

5. There is a minimum of statistical analysis. One would like to see, for instance, a phylogeny based on the mitochondrial genome or HVI regions, or even the pair-wise distances between the samples and other humans.

Authors’Response:  We have provided six mtDNA phylogenetic trees and three nuclear phylogenetic trees derived from the 3 whole genomes sequenced with next generation sequencing and have shown the pair-wise distances.

6. The authors do not follow the proper protocol for naming a new species.

Authors’Response:  We have removed any taxonomic references and have chosen to call the hominins Sasquatch.

Has anyone else been able to read the documents that were posted online?

 

https://docs.google.com/file/d/1DwVFfFOS6iX9yNQrxcSBRqRwQRn3Bkoi_3nnFDtR7-eDUkx-HOP-NjMYbG8M/edit?pli=1

https://docs.google.com/file/d/1UpuWi01e6aFefwbZtnlLVVB3q6ERADEKrdN2KFnAGaPK9mqTTrDqrjKLkm2F/edit?pli=1

 

The first is claimed to be Melba's responses to Nature's request for changes. The second is supposed to be a letter from Melba to Nature.

 

I can't read them because my laptop won't open them.

 

OK, that last one worked alright but the other one gave me fits. Here goes:

 

December 19, 2012
 
NPG Executive Board
 
Nature
 
London, England
 
Re: Novel North American Hominins, Next Generation Sequencing of Three Whole                  
 
Genomes and Associated Studies
 
Dear Executive Board,
 
I am the corresponding author for the above mentioned manuscript. We (the authors 
 
of this manuscript) are extremely unhappy with the ethics of the reviewers chosen by 
 
Nature. Please consider this letter as a formal appeal of your process on the previous 
 
manuscript, 2011-09-11671 and 2011-09-11671A-Z. We are resubmitting a revised 
 
manuscript in an effort to vindicate our reputations and also to give Nature a chance to 
 
rectify the scientific bias and the unethical behavior exhibited by the previous reviewers 
 
by giving our manuscript a fair chance at publication. Our manuscript and our reputations 
 
were tarnished by the reviewers as follows:
 
1. Release to the public of the first peer review as well as the fact that our 
 
manuscript was at Nature. One of the reviewers leaked the original peer review 
 
to a “celebrity†that is involved with our subject and it was put on the internet.  
 
Since it has not been published in Nature, this “celebrity†is now calling our study 
 
a “fake†on Twitter and elsewhere. This is highly damaging to our careers and 
 
never should have happened.  The link states the source of the information as 
 
 
2. Reviewers accused our genomes of having contamination even though we went to 
 
great lengths to explain how the samples were extracted and screened to rule out 
 
contamination. To tell us, as scientists, especially those of us that are forensic 
 
scientists, that our samples are contaminated can be likened to accusing us of 
 
hoaxing a scientific study or perjuring ourselves in court. As forensic scientists 
 
that testify in court, this can be highly damaging and has caused all of the authors 
 
tremendous worry and concern. Since we were not given a chance to defend 
 
ourselves on the second peer review and our manuscript refused because of these 
 
accusations (since all other revisions were verbiage and extremely minor), we 
 
contacted Illumina (manufacturers of the HiSeq 2000 next generation sequencing 
 
platform that we used to sequence the genomes) in an effort to prove, once and 
 
for all, that the three genomes were single source and not contaminated. We 
 
spoke with two supervisors specializing in technical support for next generation 
 
sequencing. We asked them if it was possible to prove if there was contamination 
 
in a genome or not.  They immediately answered “yesâ€!  They told us that the 
 
average Q30 score for a genome was 85, but if there was contamination, which 
 
would cause the divergent sequences to compete against one another, that a 
 
contaminated sample would have a Q30 score of only 40 to 50.  A pure, single 
 
source sample would have a Q30 score of about 85.  When we checked our Q30 
 
scores for the first read, our three genomes had Q30 scores of 92, 88 and 89 
 
respectively.  The second read was a little lower 88, 84.25 and 83.66 but still very 
 
close to the average of 85.  The Q30 is the percent of the reads that have the 
 
statistical probability greater than 1:1000 of being correctly sequenced.  
 
Therefore, with the help of the scientists at Illumina, it was determined that not 
 
only were the sequences from a single source, but the quality of the sequences 
 
were far above the average genome sequenced using their platform. I can furnish 
 
contact information if you desire it. We attribute the high quality of the genomes 
 
to the stringent extraction procedures utilized whereby the DNA was repeatedly 
 
purified.   This gave us greater than 30X coverage of the three genomes.  
 
Furthermore, it supported our original findings of human mitochondrial DNA 
 
since the whole genomes yielded human mitochondrial DNA consistent with the 
 
original individual mtDNA genome sequencing.  The nuDNA findings were also 
 
supported in that there was novel primate sequence in the nuDNA. So, the 
 
original submission was indeed supported by the next generation sequencing that 
 
we included in the revised submission. The three genomes aligned with one 
 
another also supporting that all three genomes came from the same species and 
 
they were NOT contaminated. Most importantly, the Q30 scores absolutely 
 
disproved the reviewers’ assumption that the whole genomes were a mixture of 
 
human with animal DNA contaminants.  The summary of the next generation 
 
sequencing generated by the Illumina HiSeq 2000 sequencer is now furnished as 
 
Supplementary Data 7 to support this discussion that is now included in our 
 
manuscript, Lines 544-558.
 
3. The peer reviewers failed to even read the manuscript because we were asked 
 
for data or criticized for not having data that was already in the manuscript or 
 
supplementary information.
 
Because of the ethical problems listed above, our group is therefore re-submitting this 
 
revised manuscript having addressed all of the concerns raised by the reviewers. We are 
 
supplying the authors’ response to each concern the reviewers had as proof of the bias 
 
and in defense of the manuscript.  We have corrected all of the verbiage concerns and 
 
added the definitive proof that the genomes are not contaminated. We are also available 
 
for questions and any further requested revision. We also added a conclusion concerning 
 
human hybridization likened to Neanderthal and Denisovan hybridization to satisfy 
 
Reviewer 3.  If it is preferred that the data speak for itself without theory, we will gladly 
 
remove the added conclusion. 
 
We want our findings published in Nature since it is perhaps the best journal published 
 
and our manuscript is being called the largest scientific find in the last 100 years. If it 
 
was not a Nature worthy manuscript, it would not have been given a second chance with 
 
revision, revision that we completed beyond what was asked of us. Besides fair review, 
 
we are asking for expedient treatment of our groundbreaking discovery since we have 
 
provided more proof of existence of these hominins than any manuscripts describing 
 
other novel species to date.  We also have other scientific groups that are headed by 
 
“famous†scientists still trying to beat us to publication even though we have by far 
 
the most data. We know our manuscript is worthy of publication because we have had 
 
private peer review that was positive as well as your Reviewer #1.  We just hope Nature
 
is brave enough to do what we all know is right and that is publishing this manuscript. 
 
We would also note that a new monkey was found in Africa and published recently 
 
(PLOS One: Lesula paper) with only 6.8Kb of sequence.  We have 20 samples with 16.5 
 
Kb of mtDNA and 10 more with partial sequence but enough to obtain haplotypes with 
 
most of them coming from non-human hair yielding human sequence. This includes 
 
hair from 26, the first whole genome sample. We have three whole genomes comprising 
 
millions of reads and greater than 30X coverage.  We have 2.7 million bases aligned to 
 
human chromosome 11 that are novel primate which is no small feat considering the 
 
sequence is novel and therefore difficult to align.  That is not counting all of the other 
 
disciplines involved in our manuscript including forensic hair analysis, histopathology, 
 
forensics and electron microscopy.  It has been stated that extraordinary claims require 
 
extraordinary proof.  We have provided more than enough extraordinary proof.  We 
 
even have high definition video of the donor of sample 37 sleeping in the forest and 
 
breathing at 6 breaths per minute (Supplementary Video 1).  This sample was part of a 
 
field research study overseen by a PhD in wildlife biology so we are certain of the source 
 
of this sample and the video attached to it. We have a full facial video of her also that will 
 
be released after the paper publishes. I could arrange for the Editorial board to view it if 
 
they so desire and perhaps a copyright arrangement could be reached so that one frame 
 
could be used for the cover of the journal. The face is stunning. 
 
We understand our subject is controversial; however solid scientific methods were used 
 
in this study.  We are also attaching to this letter an overview of the laboratories utilized 
 
in the study to show how the data was produced using blind studies and reproduced and 
 
verified by other laboratories (see below).
 
If there is still any doubt concerning the existence of these hominins, we are also willing 
 
to allow a representative from Nature to travel here and see these individuals personally, 
 
preferably during a full moon to increase lighting since they are primarily nocturnal.  
 
Though there is never 100% guarantee that a sighting will occur, if a few (about 3) days 
 
are allowed, we predict that the chances of seeing one of these hominins approach 99%.  
 
So far, everyone that we have invited has had an experience, including myself and some 
 
of the co-authors.  Seeing is believing and that is why we offer this opportunity.  We will 
 
do whatever is necessary to support our manuscript.
 
Thank you in advance for fair unbiased treatment of our manuscript and for accepting it 
 
in its revised format.  
 
Kind regards,
 
Dr. Melba S. Ketchum
 
Corresponding author
 
Table of Laboratories Participating in Study
 
# Laboratory   Type of Testing Paid Authorship Blind Study
 
1 North Lousiana  Forensic DNA  No Yes No
 
Criminalistics Laboratory, 
 
Shreveport LA
 
2 DNA Diagnostics, 
 
Nacogdoches, Texas
 
Extraction and DNA 
 
quantification
 
Forensic Extraction, 
 
Species Screening, 
 
Preliminary Species 
 
Sequencing and STR 
 
PP16 genotyping, 
 
mtDNA and nuDNA, 
 
testing known submitter 
 
(human) samples.
 
Hair analysis No Yes No
 
No Yes No
 
3 Southwestern Institute of 
 
Forensic Sciences, Dallas, 
 
TX
 
4 Family Tree DNA, 
 
Houston, TX
 
5 SeqWright, Houston, TX mtDNA screening 
 
6 Helix Biological 
 
Laboratory, Department 
 
of Biological Sciences, 
 
Wayne State University, 
 
Detroit, Michigan
 
7 USC, Los Angeles, CA  Whole genome Bead 
 
8 University of Texas at 
 
Arlington, Wakeland  
 
Laboratory
 
9 UNT Center for Human 
 
Identification, University 
 
of North Texas Health 
 
Science Center, Fort 
 
Worth, TX
 
10 Texas A&M University, 
 
College Station, TX 
 
mtDNA confirmation 
 
and mtDNA whole 
 
genome sequencing and 
 
haplotype assignment, 
 
PP16 STR confirmation 
 
testing and YSTR 
 
testing. Single locus 
 
Amelogenin testing
 
confirmation, sequenced 
 
various selected  
 
nuDNA loci and 
 
confirmation of mtDNA 
 
species sequencing, 
 
sequencing of various 
 
amelogenin exons
 
Blind parallel mtDNA 
 
testing of certain 
 
submitted samples.  
 
This work was done 
 
previous to our project 
 
and only became aware 
 
of this testing after we 
 
had confirmed mtDNA 
 
species ID on the same 
 
samples.
 
Array SNP analysis
 
Next Generation whole 
 
genome sequencing and 
 
bioinformatics
 
Confirmation of 
 
bioinformatics
 
Yes No Yes
 
Yes No Yes
 
No Yes No
 
Yes No Yes
 
Yes No Yes
 
Yes Yes No
 
Electron Microscopy 
 
confirmation
 
Yes Yes  Yes
 
11 University of North 
 
Carolina, Chapel Hill, 
 
North Carolina
 
Electron Microscopy. 
 
The director was 
 
unhappy about the 
 
blind study and refused 
 
recognition in the ms.  
 
He did give us the data 
 
to use.
 
Histopathology Yes No No
 
No No Yes
 
12 Texas Veterinary Medical 
 
Diagnostic Laboratory, 
 
Texas A&M University, 
 
College Station, TX
 
13 Huguley Pathology 
 
Consultants, Ft. Worth, TX
 
Histopathology 
 
confirmation 
 
No Yes No

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chelefoot

Thanks for doing that!

 

Well... interesting. During all of this we were being told...."ANY DAY!"

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Cotter

This:  "The three genomes aligned with one another also supporting that all three genomes came from the same species and they were NOT contaminated."

 

I didn't think this was the case?
 

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southernyahoo

The hostility was to the Ketchum noise, by which I stand.

 

When a scientist acts like she has, well, the results can be anticipated.  If one isn't acting like a scientist in the prep and the presentation, why expect impeccable results?

 

And towards the "they're human" conclusion right?

 

The best thing that will come from killing this Ketchum noise is another nail in the coffin of "they're human."

 

 

Do you think it is right for reviewers to leak info about a paper in review? I don't blame Ketchum a bit for standing by her work or being angry with a reviewer.

 

All that said, I understand what the reviewers wanted, the paper could have been better, but it still doesn't mean she's wrong about the DNA in the majority of the samples. A neutral person could acknowledge that. 

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Guest DWA

Well, until I know the provenance of the samples, I can have no confidence in the findings.  I need to know it came from a big guy, not a "steak;" and not knowing that, any of our DNA says contamination to me.

 

Nobody should leak anything until the press conference.  Problem is, Ketchum started it.  She was going on for months before the findings became public about hanging out with the big guys.  That stands to get you trouble, even if they are just jealous.

 

As I said:  This will be in the superfamily Hominoidea.  I'd be willing to bet that.  But I'm leaving it to the taxonomists from there.  I just thnk that the they're-human stuff doesn't give animals enough credit.  And I don't see the extensive material culture that seems a hallmark of our genus.

 

 

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southernyahoo

Well, until I know the provenance of the samples, I can have no confidence in the findings.  I need to know it came from a big guy, not a "steak;" and not knowing that, any of our DNA says contamination to me.

 

Nobody should leak anything until the press conference.  Problem is, Ketchum started it.  She was going on for months before the findings became public about hanging out with the big guys.  That stands to get you trouble, even if they are just jealous.

 

As I said:  This will be in the superfamily Hominoidea.  I'd be willing to bet that.  But I'm leaving it to the taxonomists from there.  I just thnk that the they're-human stuff doesn't give animals enough credit.  And I don't see the extensive material culture that seems a hallmark of our genus.

 

 

I think an extensive material culture would have led to their demise, their existence depends on leaving little trace. I don't believe an animal that is not sentient and not aware of this imperative could pull off "not being discovered by science" by dumb luck alone. Being human sure would explain the speech many witnesses hear, and I will not likely ever credit a mere animal with that ability.

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MIB

This:  "The three genomes aligned with one another also supporting that all three genomes came from the same species and they were NOT contaminated."

 

I didn't think this was the case?

 

 

That's a good question.   Ketchum seems to read it that way, the reviews and others challenge that.   It's possible in an area that is novel enough, one new person could indeed make a breakthrough in understanding the rest of the experts can't see, but if that's the case, she should do a better job of explaining it to them than she has.  I haven't given up on her hybrid hypothesis, it offers an elegant solution to much of the BF puzzle, at least as I see the puzzle, but I'm not very hopeful either.  I think Dr. Ketchum is sunk whether her concept goes down with her or not.

 

MIB

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Cotter

From what I understand, Ketchum pretty much has washed her hands of the whole BF thing.  She's moved on to South American mysteries, I doubt we'll be hearing or seeing anything else from her about BF.

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Guest DWA

...and that ^ should tell us all we need to know...

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southernyahoo

I think it means she's told you all she can tell you about bigfoot.  You'll either accept it or you'll have your hands full disproving it as a proponent. The hypothesis is absolutely falsifiable if bigfoot is some ape other than human.

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