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Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall


Wednesday, December 31, 2014

Oldest Stone Tools in Turkey are 1.2 Ma and made by Homo erectus


The oldest stone tool in Turkey was discovered, and it was made by Homo Erectus. A paper by Maddy et al., reports that (I quote the Abstract):


Abstract Anatolia lies at the gateway from Asia into Europe and has frequently been favoured as a route for Early Pleistocene hominin dispersal. Although early hominins are known to have occupied Turkey, with numerous finds of Lower Palaeolithic artefacts documented, the chronology of their dispersal has little reliable stratigraphical or geochronological constraint, sites are rare, and the region's hominin history remains poorly understood as a result. Here, we present a Palaeolithic artefact, a hard-hammer flake, from fluvial sediments associated with the Early Pleistocene Gediz River of Western Turkey. This previously documented buried river terrace sequence provides a clear stratigraphical context for the find and affords opportunities for independent age estimation using the numerous basaltic lava flows that emanated from nearby volcanic necks and aperiodically encroached onto the contemporary valley floors. New 40Ar/39Ar age estimates from these flows are reported here which, together with palaeomagnetic measurements, allow a tightly-constrained chronology for the artefact-bearing sediments to be established. These results suggest that hominin occupation of the valley occurred within a time period spanning ∼1.24 Ma to ∼1.17 Ma, making this the earliest, securely-dated, record of hominin occupation in Anatolia.


The tool is a piece of stone about 5 cm (2 in.) long, fashioned by the hand of a Homo erectus in Anatolia. Far from their African homeland. A clear indication that H. erectus was alive and kicking at the time (1.2 Ma) and crafting advanced tools. By the way, Anatolia gives access to Georgia on the Northeast and, Europe to the West.


H. erectus remains were found close to this site some years ago (at Kocabas - see the full text of the paper here), but the dating was not clear, but estimated at 1.1 Ma. Now we can be sure that H. erectus was living here during this period.


stone tool by Erectus from Anatolia
The tool. From the paper


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Happy 2015


I wish you all a Very Happy New Year. May 2015 be a positive year for each and everyone of us.
Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Thursday, December 4, 2014

Africans not so differentiated after all


A paper published in Nature on Dec. 3, 2014, deals with the genome of Africans [1]. I found it interesting because, against the usual mainstream belief on African diversity, it reports that: "overall differentiation among African populations was modest [...] This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6). Genes known to be under selection were notably enriched among the most differentiated loci after masking of Eurasian ancestry". [1]


So the differences are due to Eurasian admixture! and those that were not of Eurasian origin, differed because they were being selected for positively. Clearly not the kind of scenario expected if the myth of a "molecular clock" was true.


The interesting part is that regarding SNP diversity: " A substantial proportion of unshared (11%–23%) and novel (16%–24%) variants were observed, with the highest proportion among Ethiopian populations" [1]. Note that they are Ethiopians not Sub Saharan Africans which are always mentioned as being the most diverse!


This higher diversity among "Ethiopian populations, possibly suggest[s] Eurasian gene flow", furthermore, analysis "supported evidence for substantial Eurasian and HG ancestry in SSA" (Sub Saharan Africans). The Eurasian admixture in Africans was substantial: "ranging from 0% to 50%".

An interesting discovery was that of the cause of diversity:


"On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10−31). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift (P = 0.0002). Additionally, we found no evidence for background selection as the primary driver of differentiation among these loci (Supplementary Note 7)." [1]


In other words natural selection is acting to promote diversity and it is not due to "natural drift". No regularly ticking mutation clock here, what is acting is a clock ticking at higher and variable speed, prodded by Evolutionary adaptation to a changing environment.


Source


[1] Deepti Gurdasani, et al., (2014). The African Genome Variation Project shapes medical genetics in Africa. Nature (2014) doi:10.1038/nature13997



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Homo erectus were not so dum after all!


A paper published in Nature [1] reported : "The manufacture of geometric engravings is generally interpreted as indicative of modern cognition and behaviour. Key questions in the debate on the origin of such behaviour are whether this innovation is restricted to Homo sapiens, and whether it has a uniquely African origin1. Here we report on a fossil freshwater shell assemblage from the Hauptknochenschicht (‘main bone layer’) of Trinil (Java, Indonesia), the type locality of Homo erectus discovered by Eugène Dubois in 1891 (refs 2 and 3). In the Dubois collection (in the Naturalis museum, Leiden, The Netherlands) we found evidence for freshwater shellfish consumption by hominins, one unambiguous shell tool, and a shell with a geometric engraving. We dated sediment contained in the shells with 40Ar/39Ar and luminescence dating methods, obtaining a maximum age of 0.54 ± 0.10 million years and a minimum age of 0.43 ± 0.05 million years. This implies that the Trinil Hauptknochenschicht is younger than previously estimated. Together, our data indicate that the engraving was made by Homo erectus, and that it is considerably older than the oldest geometric engravings described so far. Although it is at present not possible to assess the function or meaning of the engraved shell, this discovery suggests that engraving abstract patterns was in the realm of Asian Homo erectus cognition and neuromotor control"


Our distant ancestors were much smarter than believed until now. Symbolic representations have been believed to be a more recent acquisition (H. sapiens and, more reluctantly, Neanderthals).


A smarter H. erectus is interesting, it means that 500 kya they could have not only engraved mussel shells but also, dealt with the cold Arctic climate and walked across Beringia into the Americas.

430 - 540 ky old shell with human markings. From [1]

Source


[1] Joordens, J. C. A. et al. Nature http://dx.doi.org/10.1038/nature13962 (2014). link



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Thursday, November 13, 2014

On Mutations, mutation rates and Ust'-Ishim


A week ago I read the Supplementary Information on the 45 ky old Ust'-Ishim gene sequencing and also several posts that dealt with this very interesting paper.


I was intrigued by two points: one was their estimation of human mutation rates and the other was the autosomal "diversity" of modern and ancient humans as shown in SI 12. So I decided to write a post on each of those subjects. Today's post looks into the question of "mutation rates", the diversity issue will be the subject of a future post.


Molecular clocks and mutations


It is no secret that I am very skeptical about molecular clocks which tick with a constant rate and therefore allow us to measure the timing of past events such as splits between species or the dates when a given haplogroup appeared. So please read on with this in mind: I don't trust molecular clocks.


The key issues in today's post are:


  1. Mutations in humans take place at different rates. Yes, mtDNA, Y chromosome and autosomal DNA mutate at different rates when compared to each other, and that is ok, and explainable. What I mean by different rates is that when we compare the same kind of genetic material: mtDNA against mtDNA or autosomal DNA against autosomal DNA, in different human samples, the rates are different.
  2. Genetic mutations grow at different paces in men and women.
  3. The DNA of our closest relative, the chimpanzee mutates at a different rate, when compared to ours.
  4. More genetic diversity may not mean "older" populations but simply quicker mutation rates that accumulate in a population of the same age as a less diverse one.
  5. The concept of a molecular clock is unsustainable.

The "molecular clock" that is used to estimate past events in human evolution is based on the simple assumption that: mutations take place in our DNA at a certain fixed pace and that by comparing the quantity of mutations by which specimen A and specimen B differ, we can calculate the time that has elapsed since they shared a common ancestor.


Neat. But what exactly does it mean? and even more important: is it really a clock?


First of all, lets see what a mutation is:


We are all familiar DNA and its role in inheritance. DNA is a polymer that is found inside each and every one of our cells, inside the cellular nucleus. It is shaped like two intertwining coils (a "double helix") and these spirals are stabilized by molecules known as "nucleobases" (or "bases" for short) which link the coils together.


One base is attached to one of the coils and another base is attached to the other coil; and both bond together to form a "base pair".


Fortunately these bases come in four kinds: adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T) and they link up in a very simple manner:


A only bonds with T and C only links up to G. So the "steps" of the ladder that joins the two spiral strands is made up of base pairs such as:


....
AT
TA
CG
CG
AT
GC
TA
....


During replication, the DNA strands within the nucleus of the cell, "unwind", unzipping each strand. The exposed bases attract a new pair and form the other complementary spiral. The "unpaired" Adenine will attract thymine and link to it while the guanine will bond to cytosine and so forth. This bonding takes place on each of the unzipped strands, so from one (1) initial DNA molecule, two (2) "identical" copies are obtained.


Copies and errors, causes


Well, not exactly "identical", there are some sequence errors, and this takes place even though cells have proofreading abilities and mismatch repair mechanisms that compare original and copied DNAs.


These errors in the transcription mean that the "daughter" DNAs are not an exact replica of the "mother" DNA. So maybe an AT is lost or replaced by a GC or a duplicate is inserted so TA becomes TA TA...


In other words these are natural spontaneously occuring mutations.


Other external factors known as "mutagens" can interact with the DNA and alter the nucleotide sequence producing mutations:


  • High Energy Electromagnetic radiation. For instance X-rays or Ultraviolet light (UV).
  • Oxidizing agents (or free-radicals).
  • Chemicals, such as alkylating agents, heavy metals, solvents, monomers, agrochemicals.

These factors can disrupt the sequence of a DNA strand resulting in a "new" (mutated) chunk of genetic information, either due to deletion or addition of base pairs.


There is also a process known as "Recombination" by which two DNA molecules merge in certain sections and produce a totally new variety of DNA.


Where (and when) do mutations take place?


Those terrible summer sun-burns that I suffered as a child back in the 70s, and the accumulated doses of UV radiation that my skin has received over the years, may result in a mutation that causes skin cancer (I keep my fingers crossed and visit my dermatologist once a year just in case).


The same could be said about the X-rays that have zapped me at my dentist or during my medical check-ups or the cosmic rays that incessantly criss-cross my body. Some pesticides that I ingested via fruits or cereals, those glasses of red malbec (and its metabolized by-products) or the cigarrettes that I used to smoke are also packed with mutagens... which disrupt my DNA here and there.


But all of these mutations which are taking place in some of the 40 trillion cells that make up my body would only affect me and therefore would not be passed on to future generations unless they took place in certain cells and, during a specific time frame which differs for men and women.


The new DNA information created by mutations would pass on to my progeny only if it mutated inside my "germ cells" (sperm in my case since I am a man or, for women: their ova).


Mutations that are inherited: Meiosis


Normally our cells reproduce by a process known as "Mitosis", and its outcome are two cells, each carrying the same genetic information that the mother cell had, as well as the same number of chromosomes.


We humans are dipolid organisms and as such, our cells carry two homologous copies of each chromosome, one inherited from our mother, the other from our father. Our cells therefore have 23 pairs of chromosomes of which 22 pairs are autosomes, one pair are the sex chromosomes (the X and Y chromosomes, paired XX in women and XY in men ). The grand total is 46 chromosomes per normal human cell


But our "germ cells" are different, they can only carry half of the genetic information of each parent so that the combination of the father's sperm and the mother's ovum with their chromosomes add up to exactly the full number of chromosomes.


This process of germ cell formation is known as "Meiosis", and it takes place differently in males and females:


  • Females. Meiosis in females is known as "oogonia", and consists of a series of divisions of the "original" oogonium with the complete set of chromosomes, the outcome is an an ovum with half the quantity of chromosomes.
    Meiosis in females takes place during the formation of the embryo (after the fourth week of pregnancy), as soon as the primordial germ cells migrate to the ovary, and they will lie dormant inside a protective follicle until the woman reaches puberty, when her menstrual cycle begins.
  • Males. The process in males is known as "spermatogenesis", and takes place in a continuous manner, after puberty, until death. Meiosis produces spermatozoa in the seminiferous tubes inside the testicles.

Implications


Since male germ cells are produced in a constant manner, the different mutagens that interact with an individual during is whole adult life, (meiosis is a continuous process in men) may cause mutations. Furthermore, males have a very poor DNA repair mechanism, so these mutations are more likely accumulate, without being "fixed", and therefore more likely to get transmitted to their offspring.


The female ova, on the other hand are produced during fetal growth, and are placed in hybernation for many years until the onset of puberty. But despite this long period during which external mutagens could interact with the ova's DNA producing mutations, females have a very efficient repair mechanism for postmeiotic stages which can repair DNA until after fertilization. [3]


This means that sperm accumulate more mutations than ova, and men transmit more mutations to their offspring than women do. This has been corroborated by separate studies both in humans and in chimps:


Chimpanzees, our closest relatives have different mutation rates


Chimps are our closest primate relatives, and a recent paper (Venn et al., 2014) [1] found that "mutation rates and patterns differ between [our] closely related species", Venn reported that male chimpanzees pass on between seven and eight times more mutations to their offspring than do female chimps. This means that roughly 88% of the mutations found in their offspring have a paternal origin and 12% are maternal.


Also, the older the father, the more the mutations in the paternal genes ageing adds "three mutations per year of father's age"[1].


In humans on the other hand "every additional year of father’s age contribut[es] two mutations across the genome and males contribut[e] three to four times as many mutations as females." [1], so males provide between 75 and 80% of the mutations and females 20 - 25%. /p>

This increased mutation contribution by males was reported in a genetic study by Campbell et al., 2012 [7] which found among Hutterite families that 85% of the new mutations were of paternal origin. Which is higher than those mentioned by Venn for humans and very close to those of chimps.


Campbell reported the following figures:


SNV mutation rate: 1.20 × 10-8, (95% confidence interval 0.89 – 1.43 × 10-8) mutations per basepair per generation. And 0.96×10-8 for the most recent generation.


The lower mutation rate for the latest generation was justified by "the relatively young age of the father of the trios analyzed here (21–30 years old at the time of the child’s birth)" [7], meaning that a younger father had accumulated less mutations than an older one.


Calculating Mutation Rate


The mutation rate can be calculated using the following formula:


Mutation Rate = # of mutations observed ⁄ (# of generations x # of base pairs sequenced) [a]


By comparing the discrepancies in the gene sequences of two related individuals separated by a given time span the mutation rate can be calculated (i.e. father - son pairs or comparisons of the DNA between living individuals and that sequenced from his ⁄ her ancestors).


Roach et al., (2010) [8] analyzed the full genome sequence of a family (two children and their parents) and calculated a mutation rate of 1.1 x 10-8 per position per haploid genome.


But what does this mean? Look at it this way: humans have about 6 x 109 base pairs (six billion), so it is very straightforward to work out the number of mutations that will appear in a child, inherited from its parents. They are (see [a] above) directly proportional to the number of bases, the number of generations - in this case = 1 - and the mutation rate. So, using [a] we can calculate:


# of mutations observed = Mutation Rate x # of generations x # of base pairs


So, replacing the terms with actual numbers:


# of mutations = 1.1 x 10-8 x 1 x 6 x 109


# of mutations = 66 (the new mutations in a child, compared to its parents).


Comments


Out of these 66 mutations, roughtly 80% (or 53 are parental, the other 13 maternal). Since paternal mutations grow at a rate of 2 per year [1], we can see that the child of an "old" dad aged 45 would receive 2 x (45-20) = 50 "extra" mutations in its genome in comparison to the child of a "young" 20 year old father.


So the baby of "old" dad would have 66 + 50 = 106 mutations while the baby of the "young" dad would have only 66 mutations.


Looking at a society where older parenting prevails (young males are not successful in mating with the women, or they die off before bearing children, or their children die off before reaching maturity) we would find that mutations would have accumulated at 106 mutations⁄generation. While a society where young males exclude older ones from bearing children, the mutations would accumulate at a rate of 60 mutations⁄generation.


After "n" generations the situation would be:


Old men society: n x 106 mutations. Time span: n x 40.
Mutations per year: n x 106 ⁄ n x 40 = 106⁄40 = 2.65


Young men society: n x 60 mutations. Time span: n x 20.
Mutations per year: n x 60 ⁄ n x 20 = 60⁄20 = 3.00


On a "per generation" basis there are 76.7% more mutations in the "old men" society, but on a "per year" basis, the mutation rate is 13.2% higher in the "young men" society.


This should be a word of caution when using "generations" to gauge ancient events. The conclusions will be very different in one case or the other.


The variability of Mutation Rates


The problem is that the mutaton rates are quite "variable". A paper by Wang, J. et al., (2012) [9], sequenced individual sperm cells in a 40 year-old individual. They obtained mutation rates of 2.0 to 3.8 x 10-8, which, are different from other values measured in other studies:


Hutterites (mentioned above): their "SNV mutation rate [was] 1.20 × 10-8 (95% confidence interval 0.89-1.43 × 10-8) mutations per base pair per generation." [7]


Pedigree. Xue et al., (2009) [6] compared the mutations detected in the Y chromosme of two members of the same family separated by a span of 13 generations. They reported that "The mutation rate is ... 1.0 × 10-9 mutations ⁄ nucleotide ⁄ year (95% CI: 3.0 × 10-10 – 2.5 × 10-9), or 3.0 × 10-8 mutations ⁄ nucleotide ⁄ generation (95% CI: 8.9 × 10-9 – 7.0 × 10-8)" [6] .


Just look at Xue et al.'s enormous Confidence Interval: it is almost one order of magnitude, that is the upper limit is nearly 10 times the value of the lower limit! This is like saying that we estimate the weight of the stone to be 10 pounds, with a CI of 3 lb - 25 lb.


The range between the minimum and maximum values of these studies goes from 0.89 to 7 x 10 -8 mutations ⁄ base pair ⁄ generation. A big window indeed.


Variability between families


Additional proof of the variability of mutation rates comes from a paper (Conrad et al., 2011) [5] which confirms that there is "considerable variation in mutation rates within and between families". The authors compared female and male germline and non-germline de novo mutation rates and found that "in one family [...] 92% of germline DNMs were from the paternal germline, whereas, in contrast, in the other family, 64% of DNMs were from the maternal germline." [5]


Against the constancy of mutation rates


We could imagine that additional research will refine those values and come up with a more reliable rate, but there is another problem: the mutation rate is not constant. It fluctuates accelerating and slowing down over time.


A paper by Amos W., (2013) points out a that "tendency for Africans to have diverged more from chimpanzees than non-Africans is unexpeced under classical theory." [4] Since we all derived from chimps, and have had the same time to accumulate mutations, why do Africans appear more distinct?


Applying the formula [a] it is quite simple to see that if the number of mutations is higher for Africans, then either the number of generations and ⁄ or the mutation rate must be higher for them than among non-Africans. Amos finds no reason to imagine a shorter generation time in Africa (shorter duration means more generations in a given time span). Clearly something is influencing the mutation rates in Africa.


So for Amos, this implies that the anomaly may be due to two reasons "local effects that vary across the genome due, for example, to natural selection, and genome-wide effects arising from a mutator allele impacting mutation rate or demographic influences that alter generation time." [4], the paper suggests that the mechanism that is acting to distort mutation rates is known as the "heterozygote instability" (HI) hypothesis.


Under the HI hypothesis:


mutation rate increases at and near heterozygous sites where the two homologous chromosomes differ in sequence [...] [4]


This means that "gene conversion events focused on heterozygous sites during meiosis locally increase the mutation rate [and] As humans left Africa they lost variability, which, if HI operates, should have reduced the mutation rate in non-Africans. [4]


In other words, the bottle necks that decimated humans (and also their Neanderthal and Denisovan) predecessors as they moved out of Africa and across Eurasia, led to reduced diversity and this in turn decelerated their mutation rate in comparison to those that remained in the African homeland whose diversity remained higher.


"Under the HI hypothesis, this demographically-induced reduction in heterozygosity should create a parallel reduction in mutation rate such that Africans have diverged more than non-Africans from their common ancestor" [4]


I will go over this in detail in my next post on "African diversity vs. non-African lack of diversity", but focusing on this post's subject, how does this impact on mutation rates?


Simple: mutation rate grow with increasing heterozygosity. Also "When population size is constant, smaller populations will experience lower mutation rates than related larger populations" [4].


Summary on mutation rates


DNA mutates at different rates:


  • In male or female germ cells
  • In different families
  • In less diverse populations vs highly heterozygous populations (HI hypothesis)
  • In chimpanzees (vs. humans)
  • In older men's sperm vs. younger men's sperm
  • In large populations vs. small populations

And as we will see below, ancestral DNA (obtained from the remains of ancient humans) show different rates when compared to the pedigree rates calculated by using sequences of recent modern families.


Ust'-Ishim and its estimates on mutation rates


And now, we get to the paper on the Ust'-Ishim remains (Fu, et al., 2014) [2]. Besides a wealth of data on admixture and mtDNA & Y chromosome haplogroups also deals with mutation rates, and reaches some very interesting conclusions (Below I will refer to the Supplementary Information freely available online):


Autosomal Mutation Rates Estimates


The paper measured how many mutations are "missing" in this 45 ky old individual when compared to contemporary humans. The logic behind this calculation is that we kept on evolving during that period of time and accumulated new mutations (see SI 15). Since the bone was carbon dated (41,410 ± 960 BP or 45,000 cal BP) and the substitutions can be measured, the calculation was relatively simple.


As expected, the DNA of Ust'-Ishim is around 0.6% shorter than the A-Panel (a low-coverage of 24 - 32%) modern humans and 0.35% for B-Panel samples (with a higher coverage of 35 -42%). So the autosomal mutation rates are: "0.80-0.91 × 10-9 ⁄ bp ⁄year for panel-A and 0.44-0.63 × 10-9 ⁄ bp ⁄ year for the B-panel." [2]


The authors therefore "estimate a nuclear mutation rate of 0.44 -0.63 × 10-9 ⁄ site ⁄ year, which is lower than the value that has been widely used in the past (1 × 10-9)." they do point out that the "lower quality A-panel individuals give significantly different results, indicating that this measure is sensitive to quality differences between the compared genomes" [2]


Indeed "different", the values differ by a factor of 2! Notice that they are also giving their figures in mutations per site per Year, further up, the figures we mentioned were "per Generation". Conversion from one to other depends on the time span assigned to a Generation which can range from 19 to 40 years!


Comparing Ust'-Ishim (ancestral) and Xue's pedigree values [4] there is a two-fold spread between the minimum and maximum values.


  • 0.44 - 0.63 x 10-9 ⁄ bp ⁄ year (Ust'-Ishim)
  • 0.30 - 2.50 x 10-9 ⁄ bp ⁄ year (Xue's data)

Mitochondrial DMA mutation rates


Using the mtDNA (SI 8), Fu et al., (which by the way, the mtDNA "appears to be most closely related to the direct R sub-clades R* (P, B, F, T, J)" [2]), they also estimate a mutation rate of "2.53 × 10-8 substitutions per site per year (95% HPD: 1.76 -3.23 × 10-8) for the complete mtDNA" [2]. Notice that it differs from the autosomal mutation rate calculated above by a factor of about 50 corroborating that mtDNA mutates rapidly.


Y-chromosome mutation rate


The team also sequenced Ust'-Ishim's Y chromosome and found that it "clusters with the K(xLT) haplogroup." [2], they estimated its mutation rate as "0.76 × 10-9 substitutions per site per year (95% HPD: 0.67-0.86 × 10-9)". Which was higher than the rate reported in the controversial paper by Mendez et al. (2013) which discovered a new Y chromosome lineage (A00) with a Most Recent Common Ancestor (TMRCA) of 338 ky, far older than the oldest anatomically modern human fossils.


Table S9.1, shows that the (TMRCA) for all Y-Chromosomes as 153 ky old (range: 132-175 ky).[2], since the mutation rate used is higher, the TMRCA is much more recent than the figure calculated by Mendez (153 ky vs. 338 ky).


A novel calculation of the mutation rate


Fu et al., devised a new method of calculating the mutation rate "assuming the population size history of the ancient sample is identical to that of present humans prior to the death of the archaic individual" [2] , and estimated a muation rate of 0.43×10-9 per site per year, with a 95% CI (0.38×10-9 - 0.49×10-9).


This value coincides with their estimate based on another method and is much lower than other previous values. The fact that the mutation rate is lower and therefore slower means that more time is necessary to accumulate the mutations that we carry, in other words it suggests an older date for the split between modern and ancient humans.


Another recent paper on Mutation Rates


A few days after Fu's paper, another one (Rieux et al., 2014) [10] was published, it reported an improved calibration of the mtDNA clock, and calculated a TMRC for modern humans as 143 ky (95% CI 112 - 180 ky), which agrees pretty well with Fu's estimate.


They ratified the "acceleration of substitution rates in recent times" (for mtDNA mutation rates) which is explained by the " 'time-dependency of molecular rates' hypothesis, which postulates an acceleration over recent times in coding sequences due to the time needed for selection to purge slightly deleterious mutations" [10].


They used two types of estimations, one based on the dates of the fossil remains of ancient humans (tip-based-estimates) and another calibrated on nodes, which mark peopling events such as the peopling of America, New Zealand, Madagascar, etc. They noticed that:


tip-based rate estimates are slower (by a factor of 0.63-fold) than the ones obtained using internal node calibration by Endicott and Ho (2008) but are faster (by a factor of ~1.5-fold) than previous fossil-calibrated rates
[...]
the variance over individually calibrated substitution rates is 11 times smaller for tips than internal nodes. Moreover, all of the 21 substitution rates estimated from aAMH sequences had overlapping 95% HPD (fig. 3). The situation is strikingly different for node-based calibrations, where substitution rate estimates strongly depended on the demographic episode used for dating, with only four out of ten individually calibrated rates having overlapping HPDs.
These results strongly suggest that tip calibration estimates are far more consistent than internal node-based ones. However, tip-based calibration also point to slower mean substitution rates than those based on internal nodes. Thus, one important question we need to answer is whether tipbased calibrations are affected by some systematic bias that might lead to slow (and homogeneous) substitution rates. [10]


In other words, the "nodes" or estimated dates of demographic events have a larger variance than those of the "tips" (reliably dated fossil remains). The 95% HPD interval obtained for each independent ancient sequence overlapped the others while the "nodes" only overlapped in 40% of the cases. (See their Fig. 3). The ancient remains are therefore more reliable than the estimated dates for peopling events! (something I have written about several times suggesting an ancient peopling of America). Additionally the fossils indicate a slower mutation rate meaning a more ancient date for all events (African - non-African split, Sapiens - Neanderthal split, etc.).


Rieux et al. recognize that carbon dated remains are much more reliable than the estimations of dates regarding peopling events (allow me to quote them extensively) :


the uncertainty around dated nodes is far more complex and multifactorial and is likely to lead to different degrees of reliability associated to each node. First, there is generally considerable uncertainty associated with the age of the colonization⁄migration event including error in the dating of the archaeological, anthropological, and historical evidence. The age of the oldest evidence for human presence is unlikely to coincide exactly with the demographic expansion. Very generally, we would predict to see a delay in the appearance of traces of human presence after the expansion of AMHs into any new area (Signor and Lipps 1982).
[...]
Second, even if a demographic event had been accurately dated, the age of the node in the phylogenetic tree might not coincide with it for a number of reasons (Edwards and Beerli 2000; Ho and Phillips 2009; Balloux 2010; Firth et al. 2010; Crandall et al. 2012). For instance, the phylogenetic node of interest may correspond to the most recent common ancestor (MRCA) of the sampled sequences rather than the split of the population of interest.
[...]
the population might have experienced a reduction in size later on, so that the TMRCA could coincide with this subsequent population bottleneck. We could think of additional scenarios and the situation would become even more complex if we considered a possible effect of natural selection. To summarize, node calibration can be affected bymany sources of error, and it is thus nearly impossible to model the age uncertainty around nodes satisfyingly. [10]


In other words, the nodes will give "later" dates for cases like America, subjected to a drastic bottleneck. Even so, I am quite happy to see the dates that they estimated using ancient genomes gave a much older date for the peopling of America than the usual "orthodox" 13 - 17 ky:


time peopling America
Table 2 in [10]. Coalescence Times for Major Haplogroups Involved in the Colonization/Migration Events Considered.

Yet the authors are aware of their "early" dating and try to explain the "discrepancy" to conform to orthodoxy: "However, in the case of the Canary Islands, Remote Oceania, New Zealand, and the Americas, the estimated coalescence times were systematically older than the archaeological evidence. Potential explanations for such discrepancies include ancestral polymorphism in the founding population or complex demographic histories involving multiples wavesof colonists" [10].


Finally their dating of the Divergence between Humans and Chimpanzees was 4.14 Ma (95% HPD 2.991 - 5.448). Which they admit "... may appear too young when compared with the dates that are generally derived from the fossil record." [10] . The authors attempt to explain this "recent" date as due to (i.e. "...more complex speciation scenarios where an initial split was followed by an extended period of gene flow before the final separation..."). But I do not think that it is due to a flaw in their method, but to the dissimilar mutation rates of humans and chimps, as pointed out by Venn et al., in June 2014, [1]:


Under a model in which the mutation rate increases linearly with parental age, the rate of neutral substitution is the ratio of the average number of mutations inherited per generation to the average parental age. We predict the neutral substitution rate to be ~0.46 × 10-9 per base pair (bp) per year in chimpanzees, compared to estimates in humans of ~0.51 × 10-9 bp-1 year-1 (9). These results are consistent with near-identical levels of lineage-specific sequence divergence (12) but surprising given the differences in paternal age effect. In the intersection of the autosomal genome accessible in this study and regions where human and chimpanzee genomes can be aligned with high confidence, the rate is slightly lower (0.45 × 10-9 bp-1 year-1) and the level of divergence is 1.2% (13), implying an average time to the most common ancestor of 13 million years, assuming uniformity of the mutation rate over this time (95% ETPI 11 to 17 million years; table S11). [1]


This is in agreement with the estimate of Langergraber et al., (2012) who dated the Pan-Homo divergence to between 6.78 and 13.45 Ma.


An earlier human-chimp split renders useless the calculations that calibrate molecular clocks based on that event. If it took place 13 Ma instead of 6, the clock's ticking rate has to be adjusted and all events derived from such a clock would actually be much older than currently accepted. Including the peopling of America.


More to follow, on the differing diversity of humans Africans and non-Africans


Sources
[1] Oliver Venn, et al., (2014). Strong male bias drives germline mutation in chimpanzees. Science 13 June 2014: Vol. 344 no. 6189 pp. 1272-1275 DOI: 10.1126/science.344.6189.1272
[2] Fu, Q. and many others. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514, 445-450. doi:10.1038/nature13810
[3] Andrew J. Wyrobek et al., (2007) Assessing Human Germ-Cell Mutagenesis in the Postgenome Era: A Celebration of the Legacy of William Lawson (Bill) Russell. Environ Mol Mutagen. Mar 2007; 48(2): 71–95. doi: 10.1002/em.20284
[4] William Amos, (2013) Variation in Heterozygosity Predicts Variation in Human Substitution Rates between Populations, Individuals and Genomic Regions. April 30, 2013DOI: 10.1371/journal.pone.0063048
[5] Donald F Conrad, et al., (2011). Variation in genome-wide mutation rates within and between human families. Nature Genetics 43, 712–714 (2011) doi:10.1038/ng.862. Published online 12 June 2011
[6] Yali Xue et al., (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Curr Biol. Sep 15, 2009; 19(17): 1453–1457. doi: 10.1016/j.cub.2009.07.032
[7] Catarina D Campbell, et al., (2012). Estimating the human mutation rate using autozygosity in a founder population. Nature Genetics 44, 1277–1281 (2012) doi:10.1038/ng.2418
[8] Roach JC, (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010 Apr 30;328(5978):636-9. doi: 10.1126/science.1186802. Epub 2010 Mar 10
[9] Wang J, Fan HC, Behr B, Quake SR, (2012). Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell. 2012 Jul 20;150(2):402-12. doi: 10.1016/j.cell.2012.06.030
[10] Adrien Rieux, et al., (2014). Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes. Molecular Biology and Evolution, 2014, 2780-2792, DOI: 10.1093/molbev/msu222


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Tuesday, August 26, 2014

On TB seals and an early peopling of America


My post of August 7, 2014 on Tuberculosis and the early peopling of America, was in a certain way, prophetic.


In that post, I suggested that there was a "unique" TB strain carried by Native Americans, an it arose because it was taken to the New World by Homo erectus or Neanderthals. My post wrapped up with the following remarks:


"The sequencing of the genome of the native American strain of TB will surely show that it does not share its root with the European clade. however the Amerindian strain is rare and surely overlooked in the samplings that have been carried out. Perhaps recovery of M. tuberculosis from ancient remains may provide evidence of its singular origin. We will have to wait for additional studies to prove or discard the possibility that Homo erectus or Neanderthals reached America with the ancient TB bacteria which evolved there into the Amerindian strain and back-migrated to Asia to continue evolving there."


My conjecture was confirmed by a paper published less than two weeks later (Kirsten I. Bos, et al., Aug. 20, 2014) [1] which reports that a group of scientists did just that, they sequenced the TB genome from the remains of three ancient Peruvian mummies that were over 1,000 years old, and found that the American Natives carried a very unique strain of tuberculosis, completely different to all of the Old World strains.


Of course, being mainstream scientists, they interpreted the results within the constraints of orthodoxy, and came up with some rather odd conclusions and even stranger dates. Today's post looks into this paper and its implications on the possibility of an early peopling of America by Homo erectus or Neanderthals.


Some background on Tuberculosis


Until recently, tuberculosis was believed to have been introduced to America by the Europeans after Columbus discovered the New World in 1492. The heavy death toll caused among the natives by discovery and conquest was mainly due to the devastating effects of disease (including TB).


However, evidence of Pre-Columbian tuberculosis among the natives of the New World has been suggested in several papers. A hypothesis which has been finally confirmed by this recent study [1] which sequenced DNA from Tuberculosis bacterium taken from the remains of Peruvian mummies that predate the arrival of the Europeans to America by some 500 years.


Of course, the current TB strains found in the New World are of a recent origin and were brought to America by the European influx post-1492. This European strain proved more virulent to the local natives and contibuted to their death toll, it also replaced virtually 100% of the Pre-Columbian lineages.


The Recent paper on Amerindian TB


The team which authored this paper [1] found that the Mycobacterium tuberculosis bacteria detected in the ancient Amerindian remains was not of the typical European strain, furthermore it was different to the current African and Asians strains. It is in fact very different to all other human TB clades.


The following image whcin I adapted from [1], displays the phylogenetic tree of various TB bacterial strains (both human and animal):


tb genetic tree

I added the geographical distribution of the strains [3] which in the original paper [1] are not mentioned. I did so because it provides an interesting perspective to the tree:


  • There are two distinct West African lineages L5 and L6, known as M. africanum (Shown in brown and green, respectively).
  • L1 (violet) is the strain that is predominant in South East Asia, central and southern India, and the Indian Ocean rim areas.
  • L7 (yellow) is found exclusively in the Horn of Africa (Somalia, Eritrea, Ethiopia).
  • L4 (red) is the Europan strain also found in America, where it was taken by European migrants after the discovery of the New World.
  • L2 (blue) is the East Asian "Beijing clade".
  • L3 (purple) is the Central Asian and northern India or "Delhi" strain.

The animal strains are shown in black. And the novel Peruvian "archaic Amerindian" strains in orange, on the right side of the tree.


The novelty here is the location of the Peruvian lineage, close to th TB strain found in seals, and apparently rising from the "animal" TB branches.


Animals and humans


This proximity between animal and human strains is not new, all mycobacterium lineages are classed together as the MTBC (Mycobacterium tuberculosis complex). Boritsch et al. (2014) [3] have also pointed it out: the West African strains are very close to the strains found in wild chimpanzees, to M. microti (detected in voles in the 1930s), M. pinnipedii (seals and sea lions) as well as the other strains found in cows (M. bovis), goats (M. caprae) and oryx (M. orygis). [3]


Taking a closer look at the image above, you will notice two main clusters or "clades":


  1. One composed by the animal strains plus the West African human L5 and L6 strains (and also as the new paper shows, the novel Peruvian strain [1]). They are found on the upper part of the image.
  2. The other clade comprises all the remaining human strains in Africa, Eurasia as well as the "recent" American strain of European origin (post-1492). They are found on the bottom part of the image.

This split between these two clades is defined by the "RD9-deletion" which marks the branching point between both lineages of MTBC: (i) The African-Animal (which now includes Ancient Amerindian) and (ii)the other Old World "human" strains which lack this deletion. A peculiar variety of Mycobacterium, the ancestral M. canettii marks the splitting point.


It seems that the ancestor of MTBC evolved into two separate groups, one with the RD9 deletion and the other strains, which we may call M. tuberculosis senso stricto without this deletion. This split took place during the early period of MTBC evolution (below we will see how long ago this split took place).


There is yet another split between the MTBC lines: on one side we have the African-animal-Peruvian plus L1 and L7 (East African and Indian Ocean Rim) clades while on the other we have the rest of the Eurasian strains. The split is caused by the presence or absence of a marker (Tuberculosis Deleted Region 1) or "TbD1".


This split can be seen above and also in another paper (W. Hildebrand, et al., 2008) [4], which studies the expansion of TB "Out of Africa" (O.o.A) and from which I took the following image.


The image below shows a phylogenetic tree split into two sections: on the bottom part is the "ancestral" clade or TbD1-intact (yellow) and on the top is the "modern" or TbD1-deleted strains (red).


TB tree
EAI stands for East Africa and Indian Ocean Rim

These mutatons show that the "West African - animal - Peruvian strains" are the oldest, splitting earliest from the other MTBC clades. Then come the Horn of Africa and Indian Ocean Rim variants which together with the African - animal - Peruvian strains form yet another group, and finally the other younger clades found in Eastern and Central Asia, and Europe.


Both images are anchored in an ancestral group (M. canettii or M. prototuberculosis):


The ancestral TB strain - M. canettii


There are Mycobacterium strains that live in the environment, like other microbes, in the soil or in the oceans (M. marinum or M. ulcerans), and the MTBC which live inside the cells of mammals. How did they manage to jump from one to the other? It seems that another variety of Mycobacterium, known as M. canettii is the link between environmental and human mycobacteria.


The M. canettii strain was reported in 1970 by G. Canetti in Djibouti, in the Horn of Africa. It is a peculiar strain with unusual smooth features. It is believed that it "might represent a pool of strains from which the last common ancestor of the MTBC has emerged" [3]. M. canettii and the MTBC both arose from an archaic progenitor: "M. prototuberculosis". [3]


The M. canettii genome is 20% larger than that of MTBC (+900 genes), so it shows that MTBC shed genes as it specialized in its mammal hosts.

But when did TB appear?


Dating TB


As can be expected due to the molecular clocks and dating techniques used by scientists, the published dates for the origin of TB diverge greatly: from 15 to 70 kya. [3] Furthermore, since all papers assume that TB left Africa with the "O.o.A" event with modern H. sapiens some 40 - 50 kya, this assumption constrains the dating of the different TB strains to a rather "recent" date.


But, what if it left Africa inside infected Homo erectus or the ancestors of Neanderthals, or even earlier? The ancestral home of our predecessors is in the Horn of Africa, precisely where M. canettii is currently found.


The hypothesis of an East African origin is accepted by Boritsch et al., [3] (but the dispersal vector used in the paper is H. sapiens not Neanderthal or H. erectus). Furthermore, the spread from humans to animals is also believed to have taken place in Africa, where our ancestors managed to pass TB on to chimps, dassies, oryx, cows, voles and seals: "...the animal-associated strain lineages of the MTBC seem to have evolved from RD9-deleted M. africanum-like ancestor strains that may well have been adapted to humans already".[3]


I agree with that statement, I firmly believe that these RD9-deleted M. africanum-like strains adapted early to humans, so early that we were not yet H. sapiens, but probably H. erectus or the predecessors of Neanderthals.


The trees depicted further up show very close links between the roots of the animal and West African human TB branches.


But, there is an interesting peculiarity: the oldest African strains are found in West Africa and not in East Africa the cradle of mankind. And this has to be accounted for. Below I outline a hypothesis:


The origin of TB in Africa


Let's assume that M. canettii evolved into two strains the progenitors of modern MTBC, one with the RD9-deletion which infected a "hominin". This hominin lived in Africa yet, part of that population moved out of Africa and, via Asia, reached America, where it originated the "Peruvian strain" with the RD9-deletion. Those that remained in Africa infected animal species with TB.


This explains why Peruvians, West Africans and animals share the RD9-deletion lineages. Perhaps a know extinct Asian population also had this strain.


The second strain of MTBC was not RD9-deleted, and it infected other "hominins" these lived in East Africa from where they split into a group that moved out along the coast of the Indian Ocean. This migration may represent either the Homo erectus (1.8 Mya) or the H. sapiens (100 kya) moves Out of Africa.


Finally the TbD1 deletion appeared outside of Africa and the people carrying it colonzed Europe, Central Asia and Eastern Asia, some also back-migrated to Africa. Did it appear in Neanderthals or modern H. sapiens?


The ancient African "hominin" RD9-deleted variant survived among a relict archaic population in Western Africa, long after its relatives became extinct, and only recently admixed into Modern humans in West Africa. We have already posted on the possibility of archaic admixture as the source of the extremely ancient A00 Y chromosome haplogroup, which may have originated from the introgression of "an archaic form into the ancestors of AMHs...", remains combining "both archaic and modern features" were found at Iwo Eleru in Nigeria and are quite recent: around 13 kya.


The issue is who do we assign to each migratory event.


RD9-deleted hominin could well be Homo habilis which left Africa (H. Georgicus in the Caucasus). Did they reach America? If so, the Peruvian variant could have been carried by them. The RD9-intact group could be H. erectus who remained in Africa and also peopled the coasts of the Indian Ocean. Modern H. sapiens later mutated (TbD1 deleted) and dispersed the other strains around the globe. They could also be the ancestors of Neanderthals or even modern H. sapiens.


The dating as per orthodox science is based on an average mutation rate of roughly 0.5 substitutiones &frasl genome per year. But, the issue is that TB is caused by a clonal bacteria with a very small amount of SNPs (clonal microbes tend to keep stable since they are specialized to infect specific hosts and have discarded unnecessary genes). So, can we be sure that the model used to calculate its age is really valid?


On the other hand, M. canettii has a larger genome than MTBC and around 25 times more SNPs than the MTBC lineages. So if we assign 15 - 70 ky to MTBC, does this mean that the archaic M. canettii 25 times older? That is, 125 to 1,750 ky old? [3]


It is not such a far fetched notion, in fact Gutierrez et al., 2005 [5] suggested a 3 million year date for TB.


So, we have a very wide range of dates from around 15 kya to 3 Mya. So there is the chance that an ancient hominin carried the Peruvian mutation.


Having said this, let's the conclusions of the authors of the paper on pre-Columbian TB in Peruvian mummies:


Going back to the Peruvian mummies


I mentioned above that the paper has some odd findings:


(1). "Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease" [1]. In other words, TB evolved only 6,000 years ago.


(2). Since by that time Beringia had flooded, they had to find a non-human vector that could take TB from its Source in Africa, to America. They sequenced the TB strains of different animals and found that seal TB shared similar traits with the Amerindian strain. So they concluded that seals were the source of Amerindian TB.


We can see in the images above that seal TB is one of the animal groups closest to human L5 and L6 strains. The gene sequencing conducted by Bos et al., [1] showed that the TB strains present in the Peruvian skeletons was very similar to strains of TB that are found in modern seals and sea lions.


The researchers concluded that seals somehow picked up TB from African humans and then carried it across the ocean to the New World where it spread among the native seal-hunters. [1]


I find the 6 kya date for the origin of TB too recent, and the theory of an "African to seal to Amerindian" infection route too complicated. Allow me to explain:


TB in seals


Tuberculosis in seals was studied in 2003 (D. Cousins et al.) [2], they compared genes from six species of seals taken in the UK, New Zealand, Argentina, Australia and Uruguay. They found that pinnipeds share their own strain of MTBC (Mycobacterium pinnipedii) which can also infect other creatures: "guinea pigs, rabbits, humans, Brazilian tapir (Tapirus terrestris) and, possibly, cattle" [2].


How does it spread in nature? "As with other members of the M. tuberculosis complex, aerosols are the most likely route of transmission" [2]. Seal TB is quite contagious, in fact, 6 out of 25 animal keepers at a zoo in The Netherlands became infected with M. pinnipedii when 13 out of 29 sea lions contracted the disease. [6] so no eating was necessary, just close contact with living seals was enough to pass on TB from seal to man.


But, does it work the other way round? Did Africans infect seals? or did they eat a dead Dassie or vole and became infected?


Note that African L5 and L6 strains are similar but not identical to seal TB. So it would have had to mutate in Seals and then jump again to infect Amerindians and mutate again... By the way, why didn't seals infect other seal hunting populations around the world? Only Amerindians?


Now, the interesting point is that "There seems to be a common ancestral source of M. pinnipedii across geographic locations, which raises questions about the original distribution of the seal bacillus in animals of different continents and the potential role of marine mammals in the spread and transmission of tubercle bacilli across oceans". [3]


Bos et al., assume that Africans infected seals with TB. The microbe then mutated among seals and led to a seal-specific lineage which they spread across the globe among seals and sea lions. It later infected some Peruvian seal hunters, and mutated into the Peruvian TB variety which spread among Amerindians. The image below shows this process:


orthodox TB origin

An equally valid alternative is that, as outlined above, some archaic hominin took TB to America and the seals became infected in the New World, spreading the disease among seals around the globe. The Old World variants evolved separately for a very long period of time, and this explains why Amerindian and Old World TB lineages among humans are so different:


Origin of TB in America

Taking a look at the trees above, it is clear that Seal TB branched from Peruvian TB and not the other way around. Actually the scarcity of mummy samples may have rooted Peruvians after voles instead of rooting it on the main branch, where all animal strains converge with African human ones. Perhaps futuer samples will modify the branching sequence.


Why would Amerindians, of all humans be the only ones to have evolved their strain of TB from animals. Are Peruvians the only seal hunters in the world? or the only ones that got infected?


Then there is the issue of the Dates. The researchers calculated that all modern MTBC strains date back to only 6,000 years ago.


If so, how did it spread globally so fast? By that time we were well established across the whole world!


So this means that it arrived to America between 1 and 6 kya. So, how do they account for a well known case ot TB in a 17,000 year old bison found in North America?


The bison, dated to 17,870 +⁄-230 BP had "ancient DNA characteristic of the Mycobacterium tuberculosis complex, confirming the oldest proven case of tuberculosis" [7], This bison case indicates that this disease evolved as a zoonosis in America long before the 6 kya limit established by Bos et al. Perhaps bisons (like oryx, goats, voles and seals) caught their TB from pre-Columbian humans which were already living in America 17 kya.


Sources


[1] Kirsten I. Bos, et al., (2014). Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis, Nature, doi:10.1038/nature13591, Published online 20 August 2014
[2] Debby V. Cousins, et. al., (2003). Tuberculosis in seals caused by a novel member of the Mycobacterium tuberculosis complex: Mycobacterium pinnipedii sp. nov.. International Journal of Systematic and Evolutionary Microbiology doi: 10.1099/ijs.0.02401-0 IJSEM September 2003 vol. 53 no. 5 1305-1314
[3] Boritsch, E. C., Supply, P., Honoré, N., Seeman, T., Stinear, T. P. and Brosch, R., (2014). A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent. Molecular Microbiology. doi: 10.1111/mmi.12720
[4] Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, et al. (2008). Origin, Spread and Demography of the Mycobacterium tuberculosis Complex. PLoS Pathog 4(9): e1000160. doi:10.1371/journal.ppat.1000160
[5] Gutierrez, M.C., Brisse, S., Brosch, R., Fabre, M., et?al., (2005). Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog 1: e5.
[6] Kiers A, Klarenbeek A, Mendelts B, Van Soolingen D, Koeter G., (2008). Transmission of Mycobacterium pinnipedii to humans in a zoo with marine mammals. Int J Tuberc Lung Dis. 2008 Dec;12(12):1469-73.
[7] Lee OY-C, Wu HHT, Donoghue HD, Spigelman M, Greenblatt CL, et al., (2012) Mycobacterium tuberculosis Complex Lipid Virulence Factors Preserved in the 17,000-Year-Old Skeleton of an Extinct Bison, Bison antiquus. PLoS ONE 7(7): e41923. doi:10.1371/journal.pone.0041923


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Saturday, August 16, 2014

Tarahumara Giants in Chihuahua


Reading an old magazine (Smithsonian of May 1998), I came across the following text in an article about the Mexican Tarahumara natives:

"In the 1890s, Carl Lumholtz was told a legend about a race of giants ("as big as pine-trees") that had occupied the canyon country when the Tarahumara arrived. The giants ate the Tarahumara children and ravished the women. At last, the people exterminated the giants by tricking them into eating a mixture of corn and a poisonous extract from the chilicote tree." [1]


These are interesting giants which despite being as tall as trees are sufficiently nimble to have intercourse with human women. So maybe they were giants in a metaphoric way, but size-wise they were like us.


Giants, from my perspective mean "different humans", such as Neanderthals or Homo erectus; they were the way that ancient cultures declared that a group of people were not Homo sapiens, they were men, but not like us, they were hominins. So I decided to find what Lumholtz had written about them, and below is what I found.


Giants and Tarahumara natives


Carl Lumholtz was a Norwegian explorer who travelled to Australia and Mexico. He spent many years in Mexico between 1890 and 1910, during which he spent a full year with the Tarahumara people. His book, Unknown Mexico is the source of the Giant's myth quoted below:


"GIANTS
On the heights once lived giants. They were as big as pine-trees and had heads as big as bowlders
[sic]. They taught the Tarahumares how to plant corn, by cutting down trees and burning them, but they ate children.
A woman bore a giant in a cave, which was situated very high up on the side of a valley. She died, because the child was so large, and he was taken care of by his grandmother. Once when she was asleep, she turned over and crushed him.
From Wasivori (near Cusarare) came giants to Nararachic to ask alms. Tesvino
[Note: a kind of beer made from corn] they liked very much. They worked very fast, and the Tarahumares put them to hoe and weed the corn, and gave them food and tesvino. But the giants were fierce, and ravished the women while the latter were under the influence of the Moon; therefore the Tarahumares got very angry and they mixed a decoction made from the chilicote-tree with the corn that they gave the giants to eat, and the giants died.[2]


The paragraph before the one quoted above mentions a "Deluge", which filled the world with water. It, like most Flood myths around the World (and also in the Americas) must surely reflect the deep impression caused by rising sea levels and glacial dam ruptures with the consequent flooding caused by climate change at the end of the last Glacial Period some 8 - 10 kya.


This suggests that Giants (Neanderthal) were alive at that time, in America.


These giants evidently caused problems to the human mothers bearing them, but I don't think that size was the issue (the baby's grandmother crushed the infant in bed while sleeping next to it... it wasn't a gigantic baby, it was probably a big headed child).


They were farmers but ate human children and raped their women. They lived in the mountains (perhaps in caves?), and their interactions with humans were not amicable. But, from the mythic point of vies, these creatures were not gods either, poison killed them (a tea made from the beans of Erythrina flabelliformis), they were "men".


Another source


More recently Guadalupe Holguín (2011) [3], mentions these giants as part of the "Collective memory" of the Tarahumara. They were known as "Ganokos" and were alive between 1,500 BCE and 300 CE. She mentions a giant which was known as a "uribi", which lived in Teguerichi, "with its wife and son in a cave located at Osérare. As time passed the Rarámuris [another name for Tarahumara] grew tired of him because each fertility period and crop time, this giant misbehaved and stole their food and women. So they decided to invite him to drink tesvino to get him drunk and then posion him with chilicote (a red colored bean that grows wild in the hills of Chihuahua).". [3]


Other creatures lived in the upper parts of the hills (Alta Tarahumara), like Bichiguare at Narárachi, set at an altitude of 2,290 m (7,500 ft). A very tall Tarahumara lived there, who had the same features of the "uribi" who also appeared during the crop period and also misbehaved. So he too was invited to a feast and they gave him chilicote. After that they burned him in his cave. [3]


The fact that they called him a "very tall Tarahumara" means that he was probably a giant-human (or should I say Neanderthal-human) hybrid.


Notice how all stories agree upon the "poisoning" part. These were giants that had to be exterminated. They probably competed with humans for the best crop land or for scarce natural resources during droughts. They were enemies.


Holguín says (adopting a more mainstream science approach) that thse giants are the memories of inter-ethnic strife between Tarahumara and Tubares, who were "characterized by being of a greater height than the other natives... some skeletons measure over 2 m tall" (6 ft. 7"). [3]


Lumhotz described the Tubares as enemies of the Tarahumara: "They are said to have been fierce and constantly fighting the Tarahumares..." [2], I did not find any reference to them being tall, however Holguín says that they were "very tall". [3]


Finally, Holguín adds that the Tarahumara were not alone in their beliefs about giants, the Acaxeess or Chichimecas, Chinipas, Pima and Guarojíos also believed in giants. Which she attributes to the fossil remains of prehistoric animals.


The following image [4] from the The John Lenk Collection, Tarahumara / Raramuri, Wooden Mask with White Fur Beard collected in Copper Canyon area in Chihuahua around 1965. It has a striking "hominin" appearance. The source of the image describes it as: "Copper Canyon, Chihuahua Mexico – Primitive male mask with applied fur for beard, mustache, brows, and sideburns. Roughly carved unfinished blonde wood with open mouth, peg teeth, and fearsome expression reminiscent of a Yeti or Bigfoot. Beard is white fur, possibly goat skin. Brown hair used in other areas is softer, possibly coyote or dog. Fur is still attached to tanned hide, and is delicate from age. Lots of character.". [4]


bigfoot Tarahumara mask

To close today's post, I include the following link Chihuahua mine ghost, which links to a blog post about a creature living in a mine in Chihuahua (the territory of the Tarahumara), which was reported in a newspaper back in 1892. The beast was described as: "resemble[s] a huge ape with hairy body and long, powerful arms. It is misshapen, and with deep sunken eyes...". There is even a drawing of it, representing it as a gorilla-like beast.


By the way, there are several myths (I googled them in Spanish under "fantasma mina Chihuahua" and came across several reports)on ghosts in mines in Chihuahua. Perhaps they reflect the ancient myths of primitive gigantic "cavemen" who succumbed to the encroaching Homo sapiens.


Sources


[1] David Roberts, In the land of the Long-distance runners, Mexico's copper canyon is home to the great athletes, the Tarahumara. Smithsonian, May 1998, V.29:2 - 43-52
[2] Carl Lumholtz, (1902). Unknown Mexico; a record of five years' exploration among the tribes of the western Sierra Madre. New York, C. Scribner's sons. pp. 299.
[3] Guadalupe Holguín, (2011). Asolan a rarámuris los “gigantes o ganokos”. El Observador. Chihuahua, Chih. 28 March 2011.
[4] The John Lenk Collection. Tarahumara / Raramuri Wooden Mask with White Fur Beard


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Wednesday, August 13, 2014

The Flores Island Hobbit


A brand new paper published by Maciej Henneberg, Robert B. Eckhardtb, Sakdapong Chavanaves and Kenneth J. Hsü (Evolved developmental homeostasis disturbed in LB1 from Flores, Indonesia, denotes Down syndrome and not diagnostic traits of the invalid species Homo floresiensis, PNAS 2014 ; published ahead of print August 4, 2014, doi:10.1073/pnas.1407382111 ) states that the Flores Island hominin, dating back some 15,000 years, was actually a very deformed person who very likely suffered from Down syndrome.


This is a Link to the paper so that you can read it.


I am sure that this will cause some debate and plenty of counter-arguments. If it turns out to be true, it is quite surprising, and sort of disappointing (at least for me); I was positive that it was actually a dwarf!


But let's not despair, there are still the Palau island pygmies that have to be explained... were they also afflicted with Down syndrome?


Flores skull and human skull

Above is the skull of the Flores hobbit and a modern human one.


We will have to wait and see what the final conclusions are.


NEW NOV. 2015, Another paper now says they were ancient humans evolved from H. erectus. Read my post here



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Friday, August 8, 2014

Kennewick Man, Ainus and Sunda


Two men were walking along the bank of the Columbia River in Washington, U.S. on July 28, 1996 when they came across a human skull, they quickly notified the autorities who inspected the area and, after a thorough search, managed to recover an almost complete skeleton, belonging to a man. This is how the "Kennewick Man" remains were discovered.


An initial inspection by an archaeologist [3] concluded that the man was not a Native American because the skull had a "caucasoid" appearance. A bone sample was sent to a laboratory and dated. We now know that these remains are between 8,000 and 9,500 years old. Which, by American standards is very ancient.


An act of Congress, The Native American Graves Protection and Repatriation Act (NAGPRA) was passed in 1990 with the goal of redressing the evils of the past, when Native American graves were profanated and their bones stolen and placed in Museums. The good intentions behind this legislation (which sought to return these remains to their original resting places in their tribal communities), has been distorted by the very extreme view held by some Native groups which are against any studies conducted on Paleo-Indian remains.


Actually most "modern" Native communities are relativley recent arrivals to their traditional tribal territories none go back more than one or two thousand years at most. Yet, they will go to court and in most cases succeed to get remains that date back thousands of years returned to "their homeland". In many cases the only link between the Paleoindians and the modern natives is the land where the remains were found.


Kennewick man was no exception, in 1996 some native groups took a hard stand and went to court to stop any further studies on his remains. Native American groups and the Federal Government of the U.S. combined their resources against the scientists who wanted to learn as much as possible from these extremely valuable ancient remains.


The legal battle took 8 years. In 1998 Kennewick man's bones were sent to the Burke Museum (Washington state) to protect them until the lawsuit was settled. They are still safeguarded at the Museum. [1]


The case was heard by a U.S. District Court which found that the remains could not be classified as "Native American". His ruling was appealed and the 9th Circuit Court of Appeals upheld that decision in 2004. So the remains, which were found on Federal land, are now in custody of the U.S. Army Corps of Engineers and will remain so indefintely unless the Natives can somehwo prove in the future that Kennewick was a Native American. [1]


What have we learnt from the remains?


The remains comprise an almost complete skeleton (only some bones from hands and feet and the sternum are missing) which belonged to a tall man (about 1.73 m - 5.67 ft.) between 40 and 55 years old.


Although his DNA was intact, the tests were done on two samples but were inconclusive! (more on this below).


He had the broken off remains of a flint leaf-shaped serrated projectile stuck in his right ilium (hip bone). The wound was partly healed and the stone spear tip was quite large: 20 x 54 mm (0.78 x 2.12 in), [2] however, "The extensive amount of bone that has grown around the stone point suggests that the point was in place for a considerable amount of time and was not the cause of death." [3]


The surprising part is the skull, the cranial index marks it as dolichocephalic (long and narrow skull) instead of bracycephalic (short and wide skull) as found among the modern Natives. His face was narrow instead of broad and had a pronounced chin. This and other features gave him a "caucasoid" appearance. Yet, surprisingly his teeth were Sundadont like those found among South Asians. [2]


A clay facial reconstruction gives him a very "Caucasian" look indeed, [6] below is another view of this Kennewick man's face: [7]


facial reconstruction Kennewick man
Facial reconstruction of Kennewick Man. From [7]

Sundadonty is not a Caucasian trait, it is part of the "Mongoloid dental complex" [4], which evolved locally in Sunda Land (insular Indonesia); very similar teeth are found among Aboriginal Australians which "are also generally like those of Jomonese and some Ainus, suggesting that members of the late Pleistocene Sundaland population could have initially colonized Sahulland as well as the continental shelf of East Asia northward to Hokkaido" [4].


sinodont sundadont map
Map showing the Asian Range of Sundadonty (blue) and Sinodonty (yellow).. Copyright © 2014 by Austin Whittall

East Asians to the north of Sunda (i.e. Chinese, Japanese, Koreans, Mongolians) all have Sinodonty (dental shoveling). In general people belonging to Mongoloid groups (North Eastern Asians and, also American Indians) have the highest frequency of shoveled incisors while the rest of the world has chiseled ones. Shoveling is caused by the Ectodysplasin receptor gene (EDAR), also associated with hair thickness and the size and quantity of sweat and mammary glands. It is frequent in Asian populations and absent in Europeans, Africans, Denisovans and the Mal'ta remains from Siberia who carry the ancestral allele. The mutation or introgression (admixed through direct contact with H. erectus) is believed to have appeared in central China >30 Kya, a late date in my opinion since it was obtained by simulations restrained by a 15 Kya date for peopling America, which is far to recent. [5]


His teeth


The sundadonty of Kennewick man is an interesting find because it links him to Sunda (Insular Southeast Asia) and the archaic population of Japan, the Ainus.


The map above shows a discontinuity in the Sundadont range (blue). It is the intromission of Sinodonty (yellow) which cuts off Sunda in the south from Taiwan, Hokkaido, the Kuril Islands, Sakhalin and the tip of Kamchatka in the north.


This gap is currently occupied by sinodont populations (Chinese, Koreans and Japanese).


A simpe explanation for this discontinual distribution is that the sundadonts were the original people inhabiting the coastal areas of Oriental Asia and were later overlain or displaced to their current insular ranges by sinodonts in the central region (China, Korea, Japan).


Another option is that the Sundadonts moved from Sunda northwards, along the coastal areas in boats, or walked along the now submerged continental shelf alll the way to Hokkaido -the current Ainu territory (yet they seem to have failed occupying the main southern Japanese islands, or were later displaced from there by sinodonts).


migration to America sundadonty
Map showing a hypothetical route from Sunda to America for sundadont dental morphology. Copyright © 2014 by Austin Whittall

Did a branch of these migratory sundadonts reach America before the sindonts whose dental pattern now prevails among Amerindians? or, since sinodonty is a Homo erectus trait, did the admixture leading to Amerindian sinodonty take place in America, between an early arrived sundadont H. sapiens population and the ancient H. erectus settlers in America?


Turner [8] proposes a theory where "Sundadonty or more likely proto-Sundadonty, [is] the ancestral pattern for all modern humans". He bases this on the "generalized" appearance of Southeast Asian population: "they possess various external physical features of many geographic races, although usually in relatively low frequency". Interestingly "when South Siberian teeth are compared with those of Sundadonts, they show remarkable similarities. Because South Siberian [...] hybrid condition retrodicts the probable dental pattern of the common ancestors of Europeans and Asians before these derived groups drifted to their distinctive patterns by late Pleistocene times..." [8].


So Sunda would be the source of this dental morphology, coinciding with the place from which Y chromosome Haplogroup C radiated into New Guinea, Australia, India, China and Northeast Asia. see my post on haplogroup C. South Siberians also have hg. C at low frequencies.


The Ainu


Regarding the Ainu people of northern Japan, their similarity to Sunda populations such as the Bataks of Sumatra and the Dayaks of Borneo (shee photos below) was reported back in 1872 [9]. More recently, Genetic studies link the Ainu to Amerindians, and one should reread those studies within the hypothesis mentioned above. Perhaps both groups (Amerindians and Ainu) share a common sundadont ancestor which is the main reason for the similarities detected in these genetic studies.


ainu men
ainu man
Ainu people (Notice their curly hair in the top image and the clearly non-Mongolian look of the bearded man in the bottom one)
The impression I get is that they are two different kinds of Ainu.

dayak and Batak
Batak from Sumatra and Dayak from Borneo

His DNA


The DNA samples taken from the Kennewick man did not give any conclusive results. The tests were botched (since I don't believe in conspiracy theories, I can only guess that they were done in an inadequate manner or that the technology used was rudimentary, perhaps the samples were unwittingly contaminated, etc.). Below is the conclusions by the National Parks Service [3]:


"Thus, two separate amplifications from two different extractions suggested that Kennewick Man does not belong to haplogroup D (because the fragment was at least partially digested at np 5176 by Alu I restriction enzyme) while a single amplification from one of the two extractions suggests he might belong to haplogroup D. Given that at this point it was still unclear whether or not either of the two extractions were clean (i.e., uncontaminated), amplifications from the extracts had given conflicting information and neither extract had been successfully tested for the diagnostic markers for haplogroups B, C or X, it was impossible to determine to which, if any, of the common modern American Indian mtDNA haplogroups the Kennewick remains belong. At very most, our results provided, at this point, no evidence that the Kennewick remains belonged to haplogroups A, B or C [3]


In other words he does not belong to mtDNA haplogroups A, B or C. And the two tests gave differing results for hg. D (one was positive, the other negative). So he may or may not belong to haplogroup D. He may belong to X or M or any of the other haplogroups for which he was not tested.


I have not found any records regarding his Y chromosome analysis.


Closing Comments


Despite the theories put forth by some blogs and forums regarding a European origin for Kennewick man and the links they try to build between him and the Solutreans and Cro-Magnons of Europe, I am inclined towards an Asian origin for the Kennewick man


His sundadont teeth clearly set him apart from any modern Europeans. He is closer to the more ancient modern human migrants that reached Sunda, Sahul and what is now insular Eastern Asia in the Out of Africa initial migration some 70 kya. He probably represents this basic and most archaic line of modern humans who may have reached America not long after their departure from Africa. They do not, in my opinion, represent the more recent "white Europeans" as some propose (many of these forums have some white supremacist viewpoints, which I abhor).


A clear typing of his mtDNA and Y chromosomes will settle the issue of this man and lead us to ask interesting questions regarding why are there no contemporary Caucasoid-looking Native Americans? and maybe clarify what is the exact link between these Sundadont populations, perhaps some other gene similar to the EDAR of the sinodonts?


I will dig deeper into the Ainu, they intrigue me and I want to learn more about them.


Sources


[1] Burke Museum, Kennewick Man - The ancient one
[2] James C. Chatters, (2004). Kennewick Man. Smithsonian Institution.
[3] U.S. National Parks Service Article 1, and Article 2
[4] Turner C. G., et al., (1990). Major features of Sundadonty and Sinodonty, including suggestions about East Asian microevolution, population history, and late Pleistocene relationships with Australian aboriginals. Am J Phys Anthropol. 1990 Jul;82(3):295-317
[5] My post on an Early Peopling of America
[6] Sciencephoto.com, Clay reconstruction of the Kennewick Man
[7] Chelbea Fair, The Desert Town Right Around the Riverbend
[8] G. Richard Scott, Christy G. Turner, (2000). The Anthropology of Modern Human Teeth: Dental Morphology and Its Variation in Recent Human Populations . Cambridge University Press, pp. 303.
[9] Vivien de Saint-Martin, (1872). L'ethnologie du Grand Archipel d'Asie... races humaines. L'Anée Géogr. 9:90-97



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 
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