Patagonian monsters: June 2014

Sunday, June 29, 2014

What Science is all about

A micro mini post

The latest paper on Neanderthals is one dealing with crania found at the Sima de los Huesos site in Atapuerca, Spain: Seventeen skulls were pieced together and showed a mixture of archaic and Neanderthal features. These people, were the ancestors of Neanderthals (maybe not their direct ancestors, but somewhere in their past!). They were dated to 430 kya.

But this brought to my mind another paper on Sima de los Huesos, which sequenced DNA from a 400 kya specimen (maybe one of those mentioned above), and found that they were closer to the Denisovans than to the Neanderthals!.

So one paper says the Atapuercan remains are ancestral to Neanderthal, and another says they are closer to Denisovans than to Neanderthals...

This brings me to the title of this post: science is built on discrepancies, on conflicting data. They have to be explained in a clear and rational manner that satisfies all the evidence. I expect more will come from Atapuerca and it will help us understand our human past better.

Saturday, June 28, 2014

Red headed Amerindians and the G haplogroup in America (an e-mail)

This morning I read an e-mail one of the readers of this Blog, which was very interesting indeed (Thank you for writing, Craig). My reply (edited) is below, I just wanted to share it with you because it has some good links which expand on previously published posts.

Red Headed Xiaohe mummy, China

The mail asked about photographs of the red-headed Amerindians who carried D4h3 hg. (my posts were here).

My reply

... Regarding red-haired natives, they do not abound, perhaps they were much more frequent in the past as their mummified remains attest.

If you are interested in what they looke like when photography was discovered, please check out the following sites on Alakaluf or Kaweskar, Yamana or Yaghans, Chumash, Pericue or Pericu:

http://www.limbos.org/sur/alak.htm and Kaweskar, Yamana, Chumash.

No photos exist of the Chilean Chono, who became extinct in the 1700s.

When you google red-haired native Americans you come across al sorts of weird stuff: UFOs, Atlanteans, white race supremacists, but if you remove the junk there are some nice gems to be found like the definitively red-haired Xiahoe Beauty mummy from China, pictured above, ca. 4,000 years old found in the Tarim Basin in Northwest China.

Then there are the Chinchorro people of Chile, not mentioned in my post, also boat-people like the Chumash, Kaweskar, Yamana, Chono and Peircue. Their mummies seem to be red headed. Like I mentioned in my post, these Chinchorro also used red pigment to stain their mummies and wrapped them in rushes (just like the Lovelock cave natives did).

We discussed the possible Transatlantic peopling route into America, and I commented that:

The transatlantic crossing from Africa is indeed a very feasible option (I have posted about Phoenicians, Greek and Carthagininans crossing the Ocean) and may have also been an Atlantic entry route for H. erectus into South America, so it is also possible.

I believe that mtDNA and Y chromosome analysis will reveal interesting and complex peopling patterns once the native people are sampled in depth and ancient remains are also sequenced. It willl yield some surprises. I am currenty wondering if some of the G and R Y-chromosome haplogroups found among natives is due to admixture with Europeans post-1492 discovery or... is archaic and entered America long before its discovery...

G haplogroup in America

This ends my reply to Craig, and yes, I found some G NRY hg. mentioned in a paper on the Kolla natives in Northern Argentina. The authors attribute it to admixture with Italian migrants post 1900s.

G haplogroup is definitively an Old World lineage and is found at low frequencies across a large part of Eurasia. It is also found among Spaniards (who colonized South America) and Italians (50% of Argentines have Italian ancestry), so a recent European admixture cannot be discarded.

Nevertheless, these Kolla carry a duplicate at STR DYS19, which is uncommon and found at very low frequencies in certain haplotypes within C and G Y chromosome haplogroups. C is interesting since it is a founding lineage in America but very rare and G is the European one mentioned above.

This makes me wonder.... Why do both these hgs. have the duplication and the others don't?
Could the Kolla have been wrongly typed as G and actually be C?
What are the odds of an Italian with the rare G DYS19 STR duplication reaching Northern Argentina and spreading his genes so widely that they later appear in a small sampling of Amerindian genes?
How could a genuine Native American haplotype shared with Europeans (i.e. R or G) be identified as autochthonous instead of being classified as European admixtuer(as currently is)?

I will look into this and post on it later.

Below is a map with G hg. distribution:

Friday, June 27, 2014

Y chromosome haplogroup C Part 1

C hg. in America - seeking a link with Homo erectus

The most predominant Y chromosome haplogroup among Amerindians is haplogroup Q (92.9% frequency). But it is not the only one to be found among Native Americans, there is another one, haplogroup C, which is found at a much lower 7.1% frequency among indigenous American men. [6]

C haplogroup was initially deteced in America among six populations; the North American Tanana, Navajo, Apache, Cheyenne and Sioux, and the South American Wayuu of Colombia (n = 2) [6]. And, interestingly, the haplotypes of these groups reflected their peculiarly "patchy" geographical distribution and with two very distinct clades (Patchiness appears to be characteristic with hg C., its distribution in Indonesia, New Guinea and Melanesia is also patchy):

C3b is the sub-clade that is defined by SNP P-39 and is only found in North America which means that it did not arrive "early" (otherwise it would be uniformly distributed across the New World like Q hg.), this is supported by the fact that it is found among the "latecomer" Na-Dene speakers. Nevertheless, these North American haplotypes differ among the Cheyenne, Apache and Navajo, suggesting that they had plenty of time to evolve. They have been dated to a mean age of 13,900 years [6].
C3*, Paragroup. (C-M217, which lacks P-39) is the other sub-clade, and appears in Northwestern South America and, an individual of Tlingit origin in Southwestern Alaska (presumed to be of native ancestry).

C3* is not found elsewhere (i.e. Central, North or Southern South America) and has many mutational differences separating it from the C3b haplotype, "reflecting its marked divergence". [6]

The Odd South American distribution of C3*

C3* has only been detected in three populations in South America, [2] and at low frequencies: Gepper (2011) [3] detected only 6.2% (4 out of n=65):

Wayuu Colombia. (n=2) [6]
Waorani tribe, Ecuador, (n = 3) identical haplotypes but the men were from different families.
Kichwa speakers from Pastaza province (close to the Waorani villages) (n = 11).

Close but distant. Despite proximity the Waorani were a ferocious people and until the late 1950s, they did not mix with their neighbours. The haplotypes of Kiwcha and Waorani differ by many mutations which shows that both groups "survived for a long time in isolation from each other." [2]

The patchy distribution of the C3* paragroup among isolated tribal groups and the differences that exist within these groups is suggestive. Below is a table showing the C3* among the populations mentioned above, from [2]:

Wayuu, Tlingit and Waorani differ. Kiwcha and Waorani are similar except for last three individuals (whose divergence in repeat numbers I shaded darker).

The Asian link

C3* is found at relatively high frequencies all across East Asia: Koryaks of Kamchatka (38%), Mongolia (36-38%) and it drops to 10% in Korea and 3% in Japan, yet is high among the aboriginal Ainu of Hokkaido (15%). [2]

But the Asian and Amerindian C3* are not identical: a median-joining network analysis of the Y-STR haplotypes showed that the South American C3* carriers "belonged to separate and rather distant clusters at the periphery of the network [which included Asians] , suggesting that the time of the last contact between these two groups predated the time of the initial colonization of the Americas". In other words: an ancient common ancestor back in Asia. [2] (Also see Fig. 4 in [6]).

Furthermore the Tlingit C3* from Alaska belonged to haplotype H166, the Ecuadorian Kiwcha had H7 as the most frequent haplotype followed by H162, H163, H22, but had a "substantial distance to common Asian types". The Colombian Wayuu belonged to yet another haplotype, H165, "only distantly related to the Ecuadorians" [2].

Comment. C3* is a paragroup, which means that it clumps together all C3 haplotypes that do not belong to known haplotypes for which specific markers have been identified. Since we cannot tell them apart because the chips that analyze haplotypes do not recognize them as distinct, they are all clumped together as C3*.
In other words an individual belonging to C3* in Siberia may one day be assigned to a currently unknown C3x haplotype while the Amerindians may belong to completely different yet still unknown haplotypes C3y and C3z.

Nevertheless, Roewer et al., (2013) [2] propose that the C3* found in South America is of a recent Asian origin. They believe that its limited range within America is due to a late migratory event that crossed the Pacific in water crafts and reached the Ecuadorian coasts (a boat full of Japanese shipwrecked in Ecuador that marry into the Waorani and Kiwchas...).

But first, let's look at the phylogenetic tree from Roewer et al., is very interesting [2]:

Phylogenetic tree for hg. C3*. From [2]

Some interesting points: This is a paragroup (C3*) so it encompasses all that does not fit into the know haplotypes. In other words it may include yet undiscovered haplotypes. Having said this, some relationships are clear:

The Japanese - Korean cluster (at the bottom of the tree in shades of blue). Is quite diverse and definitively separate from the American cluster (red and pink dots). Within the Japanese - Koreans we find Chinese (orange), Tibetans (brown), Indonesians (black) and Mongolians (yellow). No siberians or Northern Asians. This may indicate relationship between Southern and Eastern Asian clades concealed within the C3* paragroup.
The Mongolians appear in two distinct groups, one at the bottom, under the Japanese - Korean cluster. The other rising from the central part on the right side. This one is mixed with Altaian, Siberian, Chinese (Anatolians - white dot) and includes the Colombian natives.
The Amerindian (and Alaskan) line appears on the left, in several branches born in the central cluster it appears related to the Siberians

It seems to me that there are several different haplotypes hidden in the C3* paragroup that have yet to be identified, but the Americans, but, it clearly indicates no relationship between Japanese or Koreans and the Amerindians which is what Roewer's team suggests below.

An improbable Transpacific origin

Let's follow their arguments:

As usual the methods employed are based on the expected orthodox assumptions: 15 kya migratory event into America and a 12 kya entry into South America. [2]

Limited Distribution. "If haplogroups Q and C3* both entered the American continent from Asia at the same time 15,000 YBP, then C3* would have been expected to be more widespread than has been reported so far." [2]. My counter argument is: it reached America in a very ancient peopling wave, long before the major 15 kya event and was overlaid by the Q hg. which proved more succesful and replaced it. Another option: as it is so ancient, it is found at extremely low frequencies and that is the reason for it being bypassed by the samplings performed so far in other parts of America, a clear bias (see my post on Biases in genetic models).

However, disagreeing with Roewer' team, Zegura et al., [6] do not support the notion of two separate founding events. Instead they attribute the lower frequency of C hg. to it being a "minor component of the Y chromosomes in the single founding population" and that its frequency and patchy distribution are due to "successive episodes of intragenerational and intergenerational genetic drift" [6] in other words, they were few to start with and became fewer as time passed (more on this in my post on genetic models).

Isolated range. Since the population that peopled America came from Asia and marched in a North to South direction, if any C3* was present in that founding group, it would have to also ppear in North America and Central America; it would also be expected to have spread across South America too, like the other mtDNA and NRY hgs. too.

Since it is not found in Mesoamerica or the rest of South America, and only one case has been found in North America, yet it is very frequent in East and Northeast Asia, they conclude that it is unlikely that the initial peopling wave or America carried C3* with it. They believe that it would not get lost in the North but survive in the South if genetic drift was the cause of its loss. They also consider it unlikely that the wave carrying C#* marched quickly across North America (leaving no trace there) to settle in the south.

They summarize it as follows: the very low frequencies observed in South America "are hardly compatible with a long period of joint immigration from Asia" [2]. See above for a counter argument: two separate migratory events where the new one overlays the older one and replaces it. This is not unknown and has been pointed out in Melanesia, precisely for another C paragroup found in Indonesa and Melanesia: mentioning its ancient roots and a lower frequency as due to a "... later waves of (partial) replacement." [4].

So as an explanation for C3* being found in Northewestern South America, they propose a transpacific nautical event c. 6,000 ya, but ignore the Tinglit C3* individual in Alaska... did the Asians cross the Ocean to Peru and then go up to Alaska? or was it the other way round? Why didn't they touch land in other places and leave their imprint there too?

The 6 ky date is based on a "comparatively recent coalescence of the C3* haplotypes from the present study". [2] As expressed in my critical post on genetic models), the whole issue of dating is, in my opinion pretty feeble, so I would place a big quesiton mark on that date estimate.

They do however leave a window open when they note that the Tinglit C3* may "mean that a North American origin of the Ecuadorian C3* haplotypes, albeit less likely prima facie, cannot be ruled out" [2]. This fits in with the scenario that I propose: Tinglit is an isolated relict of the once Pan-American C3* population, later overlaid by Q hg. males of a more recent migration.

They support the transpacific contacts with similarities in the ceramics from Japan and Valdivia in Ecuador (I edited my following comment based on an input from a Reader I had mistaken Valdivia in Chile for Valdivia in Ecuador. ~~in Chile~~ and "the close proximity of the spotty C3* cluster to the Valdivia site".~~Allow me to point out that the 5,200 km or 3,200 mi. that separate the C3* in Ecuador from Valdivia are, in my opinion not a Close proximity)~~. By the way, how did the ancient Japanese mariners get to Colombia and admix with the Wayuu? That is not explained either.

New (02 July 2014), I posted on these Jomon and Valdivian contacts today so that you can make up your own minds.

Finally, and to overcome the notable differences between Amerindian and Asian haplotypes they argue that it was provoked by limited gene flow between populations and also point out that "The striking differences observed between the Y-STR haplotypes of Ecuadorian and Asian C-M217 (C3*) carriers would be explicable in terms of a long divergence time after the arrival." [in America] [5], which to me seems incompatible with the 6 ky date mentioned by them. It is not enough time to justify such diversity.

Summary: the Waorani and Kichwa in Ecuador and the Wayuu in Colombia carry a C3* paragroup not found anywhere else in America. This is an oddity that requires explaining other than a one-way-expedition across the Pacific in a boat that set off from Japan. Lets see what the Waorani and Wayuu can tell us:

The Waorani people

The Waorani or Wao people, are a small hunter-gatherer and horticultural tribe of about 1,750 individuals, that live in the Amazon jungle in Central Ecuador, South America. They are not a coastal group (which means the Japanese sailors would have had to trek inland, across the Andes into the Amazon to mate with them and get their C3* into the genome of the Wao people).

Their habitat is particular (a Pleistocene forest refugium) and is protected as a national forest. The Waorani are a highly inbred group due to their social customs: marriage with cousins is an accepted practice, [6] and social violence is the major cause of adult death (reducing availabile males for mating).

Their language -Waso Tiriro- seems to be unrelated to other regional languages, which also favors their isolation.

Besides this unique C3* NRY paragroup, they also carry a "Waorani-specific" mtDNA: A2s [6]. By the way, A2 mtDNA hg. has a strong North to South cline, similar to what would be expected for a Beringian entry and dispersal toghether with the NRY C3* hg. It is therefore likely that both maternal and paternal lineages are local and not recent arrivals from Asia.

Their isolation led them to retain this very rare paragroup which was lost elsewhere.

Tuesday, June 24, 2014

Biases in Genetic Models that are generally overlooked

Before continuing with the Y chromosome C haplogroup and its peculiar global range, I want to dedicate today's post to "Models" in general (and those used in genetics in particular), and how they shape the way we believe things work.

As an engineer I have a clear notion that a model is a simplification of the real world, we make assumptions and find that models allow us to make predictions that are reasonably similar to the real world. This allows us to build a bridge that will not collapse and yet use a minimum amount of steel, or shoot a cannon ball from A and hit a target in B. The models can be more complex (relativity is taken into account to make your GPS work correctly and quantum mechanics in all things electronic), but all of them are just that: a "model", an approximation to reality, not reality itself, merely a simplification of the real world.

Models and Genetics a critical overview

Let's review some causes of errors and the hidden biases in genetic models and methods:

Populations

Some studies use strange populations such as "MXL, Mexican Ancestry from Los Angeles USA" or "ACB, African Carribbeans in Barbados", [10] which are far less significant than a native aboriginal individual in his or her homeland: such as an "Alakaluf from Magallanes, Chile" for instance.

What conclusions can be reached on the peopling of America by looking at the genome of a person living in LA, of Mexican ancestry? Mexico has several native groups, later overalaid by Spanish conquistadors (Spanish are themselves a mixture of many ethnic groups... aboriginal Iberians, Basques, Celts, Romans Carthaginians, Arab invaders, Goths, etc.), the African slaves they brought over to work in their plantations and a touch of other European and Southern and Mesoamerican groups. In other words the Mexicans are very admixed population. MXL are actually irrelevant or former slaves of African origin living in Barbados!

Then we have studies that ignore the New World completely. Samplings cover populations in Africa and Eurasia (sometimes including Australia and PNG), seldom the Americas. This of course limits the usefulness of these studies and maybe conceals interesting findings that will remain ignored until American samples are contrasted with Old World ones.

The Sampling within the populations

Once the populations have been identified (with all the caveats mentioned above), its ancestry is studied by means of a sample of individuals that in theory (but not in practice) is drawn from it in a random manner.

In other words a sample of size "n" is taken from a population with a size "N". In most populations "N" is several orders of magnitude lager than "n" (imagine a sample of 200 Italians from Tuscany out of the 61 million people living in Italy). This implies that we may have a sampling bias, and leave out some unique or even critical genetical sequences that appear at low frequencies in a given population.

In other cases the sample is not a random one (Ascertainment bias); for instance, in the case of small tribes: the sample "n" is small because "N" is also small and perhaps encompasses a clan or family group. Thus diversity is low and, as we will see below, calculations based on these samples will be affected by this sampling bias.

Ascertainment bias also arises when researchers take samples from databases in which some populations are missing, or some regions are under represented. Or from samples obtained from volunteers (i.e. a University class) which are definitively non-random samples.

The Typing of Haplogroups in those samples

Once we have sample of our population, then we sequence the Y chromosomes (or in the case of mtDNA, the mitochondrial DNA) for known markers (remember this: known, we will get back to it later) and type the individuals based on these markers. We don't read the whole sequence of 60 million base pairs in a Y chromosome and compare them all. Instead we choose certain ones which we believe are markers and base our analysis on these markers. This introduces another ascertainment bias: the choice of markers is not random.

Look at it this way, we have a million books printed in different languages, we take a sample of fifty from the pile of books and compare them based on a few of the words printed in them: If we find the word "Chapter" we will place them in the English group, "Capítulo" in the Spanish one, "Haupstück" in the German one. All the other words are ignored. We may even find a book printed in Armenian that by chance carries the word "Chapter" and we will place it in the "English" group and ignore that an "Armenian" group even exists. We may have not sampled a Chinese book and also ignore its existence.

Yes, the analogy is faulty (well it is a model after all), the markers we look for in genetics are placed in specific locations within a chromosome. We compare the markers in specific positions with each other to define similarity. In the books example the analogy falls through because the word Chapter can appear on any page and not on a specific page. Yet, what I wanted to point out is that even though there are millions of base pairs in a chromosome, we only use a handful to define haplogroups.

Let's look at this in depth:

Y chromosome SNPs, the Haplogroups

First of all, the Y chromosomes are sequenced and the Single Nucleotide Polymorphism (SNP) that identifies a given haplogroup (hg) is identified. An example of an SNP is shown below:

AAGCCTA - ancestral
AAGCTTA - derived

The fifth nucleotide, the "C" in the ancestral variant, mutated to a "T" in the derived variant. This SNP ocurrs in a specific location. These mutations are assumed to be apparently rare, and once they happen, they remain in the DNA and are inherited by all descendants of the mutated individual. This allows us to build trees based on which SNPs are present in the populations.

The SNP that identifies the whole Hg C is marker RPS4Y711. The different haplotypes also have their own markers: M8 (for C1), M38 (for C2), M217 (for C3), M93 (for C3a), and so on.

But, as I mentioned in a previous post, it is possible that these SNP mutations revert (in that post I mention the Motala remains sequenced for a Q haplotype which lacked a key marker but had all the others), so this may also introduce additional errors.

Haplotypes and Paragroups

So, in our sample which already may have a sampling bias, we will find that most individuals will belong to a given haplogroup (i.e. Y chromosome hg C) and to a given haplotype (i.e. if they tested positive for marker M38 we will be confident that they belong to the C2 haplotype).

But... Some cases will not test positive for the known markers (i.e. M8 -excluding C1, M217 -excluding C3, M347 -excluding C4 or M356 -excluding C5), so we will assume that they form a paragroup that includes all C-other lineages, and we will identify it as C* (with an asterisk).

So these pargroups clump together a large variety of haplotypes for which we have not yet identified specific "unique" markers which would set them apart as new haplotypes.

Hidden diversity

This is not a trivial matter. For instance paragroup C* is found all across the Eastern edge of the Old World, from Australia, across Indonesia, China, Japan and India, to Bering at frequencies that range from 0.3% to 10% of the population. (some are even higher: C3* among Mongols reaches a frequency of 18% [6]).

To assume that they all belong to the same group is erroneous, the paragroup masks subclades (haplotypes) which have not yet been discovered: Maybe C* in Australia is a not yet identified C8 hg, while C* in Central Asia is a yet undiscovered C9 hg for example. In other words, there is hidden diversity out there waiting to be discovered.

Bias in the choice of the markers

The SNPs are not chosen in a random manner, they are defined by geneticists to type haplogroups. This means that the real distribution of polymorphisms in a population may differ from those shown in a study. The reason is simple: The genotyping arrays (or chips)used to identify the markers contain biased sets of pre-ascertained SNPs. These SNPs tend to be older than the majority of the SNPs in a given population, and are found in many populations besides the one being studied. These hand-picked SNPs act as sieves, classifying the samples and causing alterations such as "[shifts in] allele frequency distributions ... towards intermediate frequency alleles", furthermore, "estimates of linkage disequilibrium are modified" [11].

In other words, this increases the frequency of the most commonly polymorphic loci and eliminates other markers (loci that are less polymorphic in the screening panel). This ascertainment bias in the SNP arrays strongly skews the estimates of genetic diversity by ignoring those that are not included in them.

Variety within the Haplotypes

Once the haplogroup and haplotype have been identified, we can take a look at the Microsatellites to check out even further diversity. Microsatellites are repeats (2 to 6 nucleotides long) that repeat "n" times ( n= 5 to 100). An example: the sequence "AT" repeated 25 times in a row (this is expressed as follows: (AT)₂₅).

These microsatellites are found across species and mutate quicker than single point mutations (SNPs) and for this reason they are used as markers to define the subclades within haplotypes. An example would be a mutation in (AT)₂₅ to (AT)₂₄ or to (AT)₂₆.

In the case of our Y chromosome, we will use special microsatellites known as Short Tandem Repeats (STR). These are named as "DYS-Number" (i.e. DYS393) which indicates a position for the STR. The STR, is a series of repeats of a dinucleotide (two nucleotides).

Below is a real example, for haplogroup C, for four individuals, two from Colombia, one Korean and a Kalkh:

We can see in the image above that some DYS markers differ in the quantity of repeats (they are shaded pale blue and yellow).

The Evolutionary sequence

Now come the questions: Does the Korean derive from the Colombians or is it the other way round? What about the Mongolian? Note the differences at DYS392 and DYS393 between Koreans and Colombians (in yellow) and the difference between Colombians and Mongolians at the other DYSs (pale blue).

Without an A priori theory you can't answer that question just by looking at the repeats. Some additional assumptions are necessary, and computer programs are used to build the phylogenetic trees that link these individuals.

We could assume that humans came from Asia and peopled America, so the Americans are more recent than Asians. And as Koreans are Asians, they predate the Colombians so they accumulated mutations, passing from 11 to 12 in DYS392 and 13 to 15 in DYS393. So far so good, but then we have a Khalkh, from Mongolia, who are also Asians, but have less accumulated mutations than the Colombians or the Koreans. This way of comparing STRs is faulty.

Building a Phylogenetic Tree

The individuals are placed on phylogenetic trees using other assumptions that consider the differences between individuals, and are based on the different STRs, but it uses a different reasoning process to the one used above.

Distorting elements

Nevertheless we must remember that each DYS may have its own mutation rate, so if there are several DYS that differ, then they all have to be considered to calculate the "distance" between individuals.

An additional complication is that the "real" evolutionary history of any given set of individuals may differ from the "inferred" evolutionary history. As can be seen in the following image where only three (3) mutations out of twelve (12) are detected during analysis. The other nine (9) are ignored and remain undetected. This affects the estimations on divergence since the mutations are underestimated and the split time between the ancestor and its descendants is underestimated:

How mutations are Underestimated. Adapted from Fig. 2 in [4]

So "corrections" are introduced such as the Jukes-Cantor Model [4] which fiddle with the equations used in the models to make them fit better to reality.

So, how are the differences calculated?

Computer algorithms add even more assumptions

Algorithms are used. They are run on computers and compare the individuals in a pair-wise manner. There are several algorithms, each with their pros and cons. The two basic classes are:

Distance-Based Methods - Neighbor Joining (NJ), which initially form an unresolved star-like tree and compare the branch length sum in a pairwise manner. It then groups as "close" those that have the minimum sum. This pair is linked in a branch and then the process begins again, iterating until all individuals have been grouped.
Maximum Parsimony method, uses certain features (substitutions in the sequences) to work out a most likely evolutionary relationship among individuals. It builds the tree using the least substitutions chain from the common ancestor to the individuals being located on the tree. So it scores each possible option and minimiizes the mutation number to buid the tree.

The trees are then rooted by comparing them with some outgroup species (ie. chimpanzees are used for human and hominin comparisons). Of course this requires the assumption that molecular clocks are valid and that the divergence date with the outgroup species is well known (more on this below - see clock ticking out of time).

An example: Batwing

Batwing [8] (acronym which stands for Bayesian Analysis of Trees with Internal Node Generation), is a widely used computer program for analysis of genetic data. It has some implicit assumptions that I list below which are not mentioned in the papers that use it, but which impact on the outcome of the program's analysis. By the way, the authors of the program clearly point out that "Natural populations are unlikely to satisfy BATWING's modelling assumptions" [8].

The data is a random sampling from the population (we have seen above it is not usually the case)
The population is panmitic (not frequent in human groups)
Splitting between populations is instantaneous (actually it takes plenty of time)
There is no subsequent migration events between populations (there is always posterior admixture due to migrations between populations that have split)

Batwing uses different mutation models, but the default setting is the Stepwise Mutation Model or SSM, which we analyse in detail below.

Comment, the TMRCA (time to most recent common ancestor), Ť, is calculated under the Simple SSM model using the expression: Ť = Δ ⁄ μ.

Where Δ is the average squared difference in the number of repeats between all sampled Y chromosome and the founder haplotype, averaged over STR loci, and μ is the Simple SSM mean mutation rate per generation averaged over loci. But, if, as we will see below SSM is not very reliable, then how can clade age estimates be reliable?.

The Stepwise Mutation Model

This Stepwise Mutation Model (SSM) [2] was proposed in 1973 by Ohta and Kimura and has been widely adopted as the model for microsatellite evolution:

Microsatellites are believed to evolve neutrally: natural selection does not influence the number of repeats so, the SMM premise is: "In one generation the repeat number can only increase or decrease by one, and the probability is equal".

But this assumption is not exactly so for several reasons:

Actually, the probability of mutation is larger for longer microsatellites [1][3].
A long set of repeats (n larger than 20) may cause physical instability in the microsatellites and hamper its further growth, actually leading to their contraction. [3][2]
Some microsatellites are interrupted and have lower mutation rates.
The repeat unit also influences mutation rates: dinucleotides mutate slower than tetranucleotides.
The motif of the dinucleotide (i.e. TG vs. TA) also plays a role: certain motifs are much longer than others.
Variable mutation rates (those that change the repeat by more than 1) are not uncommon and happen about 15 to 22% of the time [3], in other words, the model ignores a big chunk of mutations.

Add to this that insertions or deletions next to the microsatellites also influence their lenghts. [3]

Even the "neutrality" of satellites is questionable since some repeats take place in promoter regions and may influence protein building [3] and thus be subject to natural selection. Some microsatellite repeats have been linked to certain diseases (myotonic dystrophy, Huntingtons' disease, etc.) making their neutrality doubtful too.

There are also "point mutations" that interrupt a repeat; an example: (AT)₁₈ may suffer a chance point mutation where "A" mutates to "G" in position 10, causing the new sequence to be: (AT)₉ GT (AT)₈. Transormation which may go undetected in sequence analysis, altering the mutation rate estimates.

Panmitic populations

Last but not least, the SMS model assumes that the individuals come from a random sample form a single panmitic population of constant size "N", and this is not the case. [5] Application to expanding populations or those with mixing due to migration may provide different results.

A panmictic population allows random mating without any restrictions of any kind (due to age, genes, behavior, social, environment, etc.), which is seldom the case in human populations, past or present.

Migrations

When an ancestral population splits into two groups, they are subjected to two opposing processes (see image below):

drift and mutation in splitting populations

Genetic Drift. It arises because N_e (number of effective breeders) which contribute their genes to the next generation is smaller than the total population, so they pass on their genes only and since this is a random sampling process, the frequency of these genes will differ from that of the previous generation. The smaller N_e, the larger the drift. This effect accumulates with each successive generation and separates the diverging subpopulations as time passes.
Migration. Exchanges between the populations as they diverge will limit the drift, keeping them similar. The proportion of migrants "m" if larger will have a higer impact on stability.

Comment on drift and lack of migration: The "Beringian Standstill" was invented to justify the strangely unique American haplogroups, completely absent in the purported Asian homeland of the Native Americans.
The Standstill theory first suggested by Bonatto & Salzano (1997) and perfected by Tamm et al., 2007, is based on a one-in-a-million "Founding effect" that isolates a group of "founding fathers" in Beringia, cut off from their Asian relatives and from the vast empty Americas by ice sheets for about 15,000 years. During this long period of time they mutated their Asian mtDNA and NRY haplogroups into new ones and then in a quick wave covered America swiftly so as not to allow new diversity to arise.
Furthermore, their Asian relatives all died off, leaving no trace on the Asian side of Beringia.
Yes, I know it sounds improbable, yet even though the odds are against this kind of event, several papers apart from Tamm et al, support the theory.

But let's get back to the Stepwise Mutation Model: it is quite weak, to put it mildly.

Summary: SMM is unreliable

All these phenomena make SMM a very rough approximation to reality, yet it is used as if it was 100% reliable!

Just as an example of this lack of reliability is the quote below (Nebel a., et al., 2001) [7]:

"the behaviour of DYS388 appears to be inconsistent with the SMM, as was shown in two populations of Middle Eastern origin. Additionally, another widely used microsatellite, DYS392, has recently been demonstrated to deviate from the SMM" [7]

The Clock that ticks out of time

I have posted on the useless genetic clocks in the past, so I will not bore you, just highlight my previous objections to clocks:

Divergence from Chimps. Scientists devise clocks to calculate mutation rates. To do so we estimate the divergence dates of the human line from the chimpanzee line. But the date of this event is uncertain, and has been increasing since the 1970s from an estimated 5 Mya to 6 - 7 Mya, and in June 2014, to 13 Mya [9], this recent change should surely impact on the dating of human origins!

Assumptions are also made regarding the duration of a generation (what can we know about how long a generation was 50 kya? did females mature earlier or later? what about males? was it 27 years or 35?). Population sizes and their trends (expansion, migration, admixture with other groups as well as bottlenecks and founder effects) also should also be factored in.

When those clocks are calibrated against real mutation rates measured in (again a discrete sample) familes over the last few hundred years strong discrepancies arise: these family (pedigree) calculated mutation rates usuall differ from the former ones (evolutionary). But these differences remain unexplained in the papers. They merely show both figures but avoid explaining the causes (i.e. the mutational clock does not tick at a regular pace).

The mutation rates are also calibrated against the estimated dates for the peopling of certain regions based on the information provided by archaeology. i.e. 40 kya for Australia or 17-20 kya for America. However just by looking at the published error margins we can see the uncertainty involved in these calculations.

Diversity is taken as an indicator of antiquity so if Region X has a large variety of haplotypes while Region Z has fewer, population in Z is assumed to be younger. But, actually what happens is that if the people in "Z" are a subset of population from Region "X", the fact that they are a subset means that they will have less diversity than the original group. This does not mean that they are more recent, it means that they left certain genes behind. Add to this the pressure of natural Selection (and chance i.e. genetic drift) and the genes of certain individuals within the subset at "Z" will get lost too. So if we measure "X" against "Z" by their diversity we would incorrectly judge "Z" to be more recent, when they are really just as ancient as "X".

Frequency, Migrations and antiquity

Often the current distributions of haplogroups occur at differing frequencies in certain territories. What does this mean? That the less frequent "A" hg is a recent arrival of a small group carrying it, entering the territory of the prevailing "B" hg.? Did "A" exist in the same population as "B", but in very low frequencies, and those have been maintained or even decreased?

Or is "A" an ancient colonizer that suffered attrition over thousands of years and has been gradually losing ground to better equipped newcomers with hg. "B"? Maybe "A" and "B" were found in equal proportions in the original colonizers but "B" grew due to genetic drift or natural selection...

Questions like those are seldom asked or answered in mainstream papers. It is clear that the choice of the correct answer requires an in depth analysis which is not found in the academic literature (I have read tens of papers and these matters are not even addressed).

The low diversity among Amerindians is always invariably attributed to a founder effect or a bottleneck during the peopling of America event. The massive death of millions of Natives (virtually a genocide) during the process of discovery and conquest of the New World between 1492 and 1560 is ignored. Disease and war acted selectively wiping out tribes without leaving a trace of them, but this issue is simply ignored and the "lack of diversity" is assumed to be due to the original peopling event some 15 kya.

Dogma

The unidirectional migratory route from Africa to the World has some inconsistencies which can only be explained by back-migrations. These into Africa migrations are reluctantly accepted by orthodoxy but, fortunately, are gradually altering the OoA picture with a more parsimonious explanation. Sometimes I get the feeling that OoA is supported because it is politically correct and assuages the guilt complex of the Western world for the tragic crimes of Slavery and colonialism perpetrated against Africa.

Two issues requiring a serious review are: The East Siberian void of putative ancestors to the Amerindians, which remains unexplained and The "Beringian standstill" justification for Amerindian uniqueness, which also requires a critical analysis due to its improbability.

Closing comments

What I have tried to express in today's post is that there are many assumptions underlying the "facts" expressed by mainstream geneticists regarding human diversity and evolution.

Models are simple representations of reality and not reality itself. They should be taken as such and not as truth written in stone.

Algorithms and simulations run on models are only as reliable as the models they are based on. And we have seen the flaws in some of these models and programs. Flaws that introduce errors in their output yet are not explicitly mentioned in the papers that basethemselves on them.

The complexities in the statistical assumptions mentioned in papers (those pages or paragraphs, full of equations that you skip when reading a paper) mask some very evident biases that skew the results and produce patterns that do not correctly reflect reality, which is richer and much more varied than what these papers show us.

Sources

[1] Esra Ruzgar and Kayhan Erciyes, Phylogenetic Tree Construction for Y-DNA, Haplogroups.
[2]Amke Caliebe et al., (2010). A Markov chain description of the stepwise mutation model : Local and global behaviour of the allele process. Journal of Theoretical Biology 266(2010)336–342
[3] Peter Calabrese and Raazesh Sainudiin, (2004) Models of Microsatellite Evolution
[4] Yan Li, Phycs498BIO Assignment 2, How to Build a Phylogenetic Tree
[5] Valdes, Ana M. Slatkin M. and Freimer N., (1993). Allele Frequencies at Microsatellite Loci: The Stepwise Mutarion Model Revisited. Genetics 133: 737-749 March 1993
[6] Boris Malyarchuk, et al., (2010). Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Annals of Human Genetics (2010) 00,1–8 doi: 10.1111/j.1469-1809.2010.00601.x
[7] Nebel A., et al.,(2001). Haplogroup-specific deviation from the stepwise mutation model at the microsatellite loci DYS388 and DYS392. Eur J Hum Genet. 2001 Jan;9(1):22-6
[8] Ian Wilson, David Balding and Mike Weale, (2003), Batwing User Guide. See pt. 1.2.
[9] 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
[10] www.1000genomes.org.
[11]Lachance J, Tishkoff SA. et al., (2013). SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. Bioessays. 2013 Sep;35(9):780-6. doi: 10.1002/bies.201300014. Epub 2013 Jul 9.
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Monday, June 16, 2014

MAPT Gene, H. habilis or H. erectus and Amerindians

AAlways on the lookout for "anomalies" in global distributions of genetic markers I came across another one which has a very high frequency in two areas and a void in between: The high frequency area is Europe, Southwestern Asia and North Africa, in other words, the homeland of Neanderthals and the areas where they or humans with Neanderthal admixture later migrated to. The other "high" (though it is quite low indeed) frequency region is South America. The void is in East Asia and Siberia.

The authors of the paper describing this gene (Donnelly et al., 2010) [1] mention the possibility of a Neanderthal admixture in modern humans.

The gene in question is the MAPT (for: microtubular associated protein tau) gene; it is classed into two families of chromosomes, the H1 and the H2 haplotypes:

H1 has been widely studied because of its close relationship with several neural disorders such as Alzheimer and Parkinson diseases as well as a variety of palsy and sporadic fronto temporal dementia. [3] [4] H1 is the most frequent variant among modern humans and is found in all human populations at frequencies ranging from 100% to 70%. It has evolved into several sub-haplotypes (H1a to x).
H2, is the ancestral variant (and is found in gorillas and chimps); it is also known as "inversion haplotype". It is found at variable but low frequencies across the globe (0 to 30%), with a marked cline as you move away from Western Eurasia and North Africa. H2 is associated with a higher fecundity rate and is believed to be positively selected for. [4]

A discontinuous distribution

The highest global frequencies for H2 are found around the Mediterranean Sea (ranging from 13% in North African Mozabites to 37.5% in Sardinians), decreasing to between 15% and 24% in more distant European areas. Elsewhere it is a lower frequency haplotype: 4% in Mandenkas, 0.7% among Biaka Pygmies and between 2& and 12.2% in most of South West Asia.

It is found at "extremely low frequencies in three populations (Mongols, Taiwan Chinese, and Japanese) and could be the result of admixture or just a very low frequency in the region". Siberians do not carry the H2 haplotype nor do the North American Cheyenne or Pima (both from Arizona and Mexico).

In North America, where Y chromosome R is found among natives and this is explained as caused by admixture with English, Spanish and French colonization, this H2 haplogrop is absent. This clearly shows that it was not introduced by the Europeans otherwise it would have admixed just the same way as R haplogroup did (unless R hg is not European, and entered America as one of the founding Haplogroups during the peopling of the New World, via Asia).

Amerindians' frequencies are around 6.4 % (Mayan and Quechua) dropping to 1.1% (Rondonian Surui) and zero among Ticuna, Guihiba and Karitiana. The presence among South American Natives is, according to the paper, due to historical European admixture.

I differ: if Europeans (i.e. Portuguese or Spanish Conquistadors mixing with the natives) were the source, we would find it uniformly spread out across the former Spanish and Portuguese colonies in America. Instead it is absent in Mexico, SW USA, Mesoamerica (excluding the Maya), Colombia and Venezuela, Argentina and Chile, Brazil...

Furthermore, only certain native groups carry it, others do not. This is a clear indication of its ancient origin and survival among Native Americans prior to the arrival of Europeans.

The map shown below depicts the global range and frequencies. Notice the absence of H2 hg in Siberia, the purported ancestral home of Amerindians.

MAPT gene H2 Haplogroup global distribution
Adapted from Fig. 3 in [1]

The Neanderthal connection

Donnelly's paper tries to identify the place where this H2 haplogroup inversion took place. The authors propose three scenarios:

African scenario, with an Eastern or Central African origin and its dispersion in an OOA event.
Southwest Asian origin, in this case it flowed back into Africa explaining its current presence there.
Neanderthal origin. They point out that this hypothesis was first suggested by Hardy et al., [2] and it explains a SW Eurasian origin since that was the homeland of Neanderthals and also the highest global frequencies which are found in the Middle East.

Hardy et al. had written: "We suggest that a plausible explanation for the ingress of the H2 haplotype is that an ancestral H. neanderthalensis allele, [...] entered the European H. sapiens genome during the period of co-existence, and has spread through selection pressure to its current allele frequency of approx. 25% in this population " [2].

However Donnelly et al. are cautious and do not favor this scenario:"Though we think that this scenario is unlikely, more evidence is needed with respect to Neanderthal’s genetic contribution to modern humans before any strong conclusion can be made. Once again, this scenario can best be addressed once the Neanderthal genome is completed." [1].

The recent sequencing of the Neanderthal genes has now allowed us to settle this issue definitively:

No Neanderthal or Denisovan H2

The remark about high Middle Eastern frequencies is interesting, especially its peak of 31% among the Druze who, incidentally are believed to be the source of the mtDNA X2 haplogroup mentioned in my previous post as a potentially Neanderthal mtNA, or, (As I will explain in another future post, probably the mtDNA of some even older hominin, below I also hint at this possibility).

The time frame proposed by Donelly et al., favors a possible Neanderthal admixture because it spans a wide period: 16,400 to 108,400 years BP, plenty of time for Neanderthal - human admixture. [1]

Fortunately for us all, two years later (2012), Setó-Salvia et al., [4] used the Neanderthal and Denisovan gene sequences to study the matter and discovered that:

"both hominins harbored the H1j variant [which] represents ~ 1.7% of all possible subhaplotypes in present-day humans of European ancestry" [4]

This finding disqualifies both a Neanderthal or a Denisovan origin for the human H2 haplogroup and the authors conclude that the inversion to H2 arose within the modern human lineage.

Interestingly, the H1j that those hominins carry, has not been correlated to neurodegenerative diseases in modern humans and the paper suggests that H1j introgressed into us due to admixture with Neanderthals or Denisovans.[4]

The paper points leaves the door open to finding H2 in our ancestors because the "data from both Neandertals and Denisova are scarce, we cannot discard the existence of H2 chromosome carriers" among both hominins. [4] I was disappointed, I really believed that our H2 came from Neanderthals.

How about an even more archaic Homo as the source of H2?

But I have not lost hope: Setó-Salvia et al., found "68 intronic variants within the MAPT gene, 23 exclusive to Denisova hominin, 6 limited to Neandertals, and 24 exclusive to present-day humans." [4]. This is a lot of variation and that requires time to develop, H1 must have diverged from the ancestral H2 longer ago than the 16.4 - 108.4 kya suggested by Donnelly. [1] And this may mean that H2 is indeed an ancestral form, found in an even older ancestor that made it out of Africa into SW Asia and Europe: Homo erectus.

Both Donnelly and Setó-Salvia cite previous work (Stefansson et al., 2005) [5] which gave an even older date for the inversion of the ancestral H2 form to the H1 found currently in modern humans (and also in the othere extinct branch of Neanderthals and Denisovans).

Steffansson set the inversion H1 into H2 at ~2.3 million years ago. And this was long before there were any modern humans, Neanderthals or Denisovans around.

However Donnelly et al., dismissed the date because the H2 lineage found nowadays in humans is very homogeneous while H1 is very diverse, so they suggest that H2 is younger since and had less time to evolve and diversify. But this may not be the case since H2 offers some reproductive advantages (enhanced fertility) as well as none of the negative neurological aspects provoked by the H1 haplogroup. The fact that it is uniform may indicate positive natural selection at work, or a strong genetic drift among modern humans after they admixed with an H2 carrying ancestor.

The image below shows this new scenario of admixture with an even older ancestor:

Proposed evolutionary tree for H1 and H2 haplogroups of MAPT gene
Adapted from [4] by Austin Whittall

Based on the date 2.3 Mya, there are not many options to choose our ancestor from: either H. habilis or H. erectus. Both left Africa, the former went on to the Caucasus and were probably ancestral to H. erectus in Asia and later Denisovans. The latter spread out across South East Asia and reached China where it has survived until quite recent times.

The lack of H2 among humans in the H. erectus territories in Indonesia, China and S.E. Asia may mean that our vector is H. habilis, from Dmanisi in Georgia. Or it may mean that the humans that introgressed with them did not later move on into Southeastern and Eastern Asia. But did march on into America or did the H. sapiens that reached America pick up the H2 haplotype there, from a first peopling wave of H. habilis?

This could be settled with a gene sequence from H. erectus or H. habilis. Perhaps one day it will be done.

Source

[1] Michael P. Donnelly, et al., (2010). The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans. The American Journal of Human Genetics 86, 161–171, February 12, 2010. doi: 10.1016/j.ajhg.2010.01.007
[2] Hardy, J., et al., (2005). Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens. Biochem. Soc. Trans. 33, 582–585.
[3] MAPT microtubule-associated protein tau [ Homo sapiens (human) ] Gene ID: 4137, updated on 8-Jun-2014
[4] Setó-Salvia, Núria et al., (2012). Using the Neandertal and Denisova Genetic Data to Understand the Common MAPT 17q21 Inversion in Modern Humans. Human Biology: Vol. 84: Iss. 6, Article 1
[5] Stefansson, H., et al., (2005). A common inversion under selection in Europeans. Nat. Genet. 37, 129–137

The first people to leave Africa and genes

This is the first post of a series which will deal with a possible archaic origin of the Y chromosome C haplogroup in humans. The idea surfaced in my mind while looking at the migratory route purportedly taken by modern humans when they left their homeland in Africa some 60 to 70 kya. After crossing the Bab-El-Mandeb Strait at the southern tip of the Red Sea, they stuck to a coastal route and advanced into Asia along the shores of Southern Arabia. After crossing the Persian Gulf at the Strait of Hormuz, the old a group carrying the C haplogroup in their Y chromosomes took a Southeastern direction, towards South Asia, other groups went North and East. mtDNA haplogroup M also split at Hormuz from N, and took exactly the same Southern path towards South East Asia.

I recalled that Homo erectus had inhabited this part of the world and wondered if there was a link between these apparently disconnected events.

I prepared a map (below), showing this migratory route where the initial OOA episode is the blue arrow and the C haplogroup dispersal is shown in red arrows. The yellow shaded regions are those where C hg is currently found:

Occam's razor to seek simple answers

The simplest explanation is this: humans are intelligent beings that follow corridors offering food, water and shelter. It is very likely that H. erectus took this coastal route because it offered all three elements and thus guaranteed survival. The modern humans that followed them 1.5 My later had the same needs and would have taken the same route if it continued to provide a competitive advantage.

So, it is not a coincidence but a logical series of factors that caused H. sapiens carrying haplogroups M (mtDNA) and C (Y chromosome) to follow the same path as H. erectus did one and a half million years earlier.

But there could be an alternative explanation to these coinciding dispersal routes: H. erectus carried the M and C haplogroups with them as they migrated along this route... and this post (and some others to follow) is the outcome. Yes, I must explain why I believe that these haplogroups even existed 1.5 Mya and were to be found in non-sapiens hominins...

The first to leave Africa

That our oldest ancestors evolved in Africa is not questioned (and it will not be questioned here either) because there is ample proof of ancient remains dating back several million years. The Australopithecines are undoubtably our most primitive relatives, and we evolved from them and their descent.

The appearance of an intelligent mind soon led to the manfacture of stone tools and the urge to discover new horizons beyond their original homeland. The existence of appropriate ecological setting and adequate resources to sustain them, enabled our hominin ancestors to move out of Africa and into Eurasia roughly 2 Mya.

The formerly accepted picture was that Homo habilis and their predecessors were too small and primitive to cope with the complexities of migrating out of Africa. Their Mode 1 flake and core stone tools (Oldowan industry) were too rudimentary. Furthermore, the dating of Asian sites showed that they were not older than 500 - 800 kya., long after the disappearance of H. habilis.

So it was their succesors, the H. erectus, who made it out of Africa first. They took their Mode 2 (or Acheulean) toolage with them into Western Eurasia yet those who went beyond India (crossing the "Movius line") and entering China and India, somehow did not use these stone tools.

But then a series of findings in Eurasia have upset this neat scenario:

Israel. 'Ubbeidiya site, in the Jordan River valley. 1.4 - 1.6 Mya. Tools with Flake and Core Mode 1 similarities. [1][2]
Dmanisi, Georgia. Crania, bones and tools (1.78 Mya) with Oldowan affinities or maybe even pre-Oldowan since many lack retouching. The remains are similar to the African H. erectus (known as H. ergaster) but have smaller crania and therefore closer to H. habilis. This suggests a pre-erectus dispersal: [3]
♦ Skull sizes from 546 cm³ to 730 cm³ vs. H. habilis' 509 to 687 cm³.
♦ Small bodied: 146 to 166 cm, 47 to 50 kg, similar to H. habilis but in the lower range of H. erectus.
Pakistan, Pabbi Hills, with a Pre-Acheulean assemblage of 2.2 - 0.9 My.

This of course upsets the previous picture: if the smallest and most primitive H. erectus remains are found in Georgia then, they may have evolved there from even earlier hominins (H. habilis), and dispersed from this point towards Africa (an Into Africa Migration) and Eastern Asia. Since Indonesian remains are about 1.8 My old, then the dispersal took place quickly. [4]

This means therefore not one or two, but multiple migratory waves: H. habilis OOA, archaic H. erectus movin on towards Asia. And maybe, even into Europe (1 - 1.2 Mya).

Mode 2 Acheulean tools are found in Africa 1.8 Mya, and later in the periphery, does this mean that they originated in Africa? : Isampur India (1.2 Mya), 800 kya in China and Ngebung, Java. Europe sees them 600 - 700 kya; Eastern Europe and the Caucasus is late (after 300 kya). [5]

This is under debate: the large flaked core (piece R001) from Riwat, Pakistan was dated [6][9][10] to the Olduvai event c. 1.8 Mya. It is different to the other tools from Africa, Europe or China. It is old yet clearly Acheulean and maybe even older than African tools.

This has suggested that Eurasia may have played an active role in the shaping of our hominin ancestors: with speciation taking place there and migrations back into Africa with subsequent dispersals just like happened with certain mammals: "more taxa migrating into than out of Africa" [7].

This would allow the African H. ergaster to have originated in Asia.

The Migratory Route

We can envisage a route from East Africa across Ethiopia and into Saudi Arabia: This would be the main exit route from Africa in an H. erectus OOA event. Yet no remains have been found, only Acheulean tools at two separate sites: one close to the Red Sea (Wadi Fatimah), another at Daw Ädmi. Unfortunately no dating is provided. [8]

As seen above there are tools but no remains in Pakistan; the next sites should be in India:

India

The earliest fossil remains and Acheulean handaxes in India are from Hathnora in Narmada Valley, Madhya Pradesh. The Middle Pleistocene (c. 500 kya) skull of an H. erectus was discovered there in 1982. [18]

The date is much later than other remains from sites in Western and Eastern Asia. So it is likely that H. erectus reached India 1 My before the Narmada remains.

Expansion after India

There are other H. erectus sites in Indian Subcontinent: in Nepal (Satpati) in the North, Attirampakkam in the South (1 Mya) and the centrally located ones at Hunsgi-Baichbal, Anagwadi and Godavari.

H. erectus continued advancing east, closed in by the Himalayas on the North reached current Myanmar. From here there is a split, in two directions, one North, into China, another South towards Indonesia.

The Southeast Asian H. erectus

Indonesia. It was on the banks of the Solo River in Java, that Eugene Dubois discovered the remains of the first H. erectus in 1891. He named the species Pithecanthropus erectus or "Upright ape man".

It is probably distinct from the African H. ergaster and the oldest remains are those found at Mojokerto (skull) 1.81 Mya and Sanigran (1.6 –1.7 Mya).

H. erectus thrived in Indonesia until quite recently: the remains from Ngandong and Sambungmacan in Java are the youngest H. erectus fossils ever found. They have been dated to between 40 and 70 kya. This means that they were coeval with the Homo sapiens that entered Australia and Southern Asia. [12]

These late H. erectus, when compared to those from other sites, are "the most derived population" [4] and have brain volumes larger than previous Indonesian H. erectus, closely approaching the mean values of extant Australian Aboriginals [13].

Their persistence until such recent times both here and in China (see below) is surprising and it raises the question of why did they disappear in Africa if they were so well adapted to survive?

Australia

No H. erectus fossils have been found in Australia. Nevertheless, robust H. sapiens remains showing possible signs of admixture were found there in 1982: the Willandra Lakes Hominid (WLH) 50. They date to between 12.2 and 32.8 kya and are clearly Human but with singular features: stron brows and thick cranium. [14]

They have a statistically significant [13] correlation with the Ngandong fossils and both may share a common ancestor with modern Native Australians. In other words they are linked to each other by "a reticulating evolutionary relationship" [13].

The Northeast Asian H. erectus

Other groups moved north, towards cooler climes in China and Korea.

South Korea, the Imjin-Hantan River Basins (IHRB) have yielded Acheulean biface handaxes. The dating of the sediments that contain them indicate that "the earliest hominin occupation of the IHRB may be slightly older than the 350 ka" [15]. Not tremendously old, but clearly pre-sapiens.

China a long persistence of H. erectus

The famous Peking Man, from the Zhoukoudian site close to Beijing, was discovered in the 1920s and named Sinanthropus pekinensis (Peking Chinese Man). The remains originally believed to be c. 300 ky old have been pushed further back: 750 kya.

China has several sites with archaic toolage: Bose, Luonan and the very ancient Nihewan site, at a high northern latitude, dated to a mean age of 1119 +⁄- 139 ka. [16]

As in Indonesia, Homo erectus survived until recently at the Lantian site close to Xi'an in Northern China; Acheulean assemblies dated to between 70 and 30 kya have been found there, suggesting the suvival of H. erectus there until " the later period of the late Pleistocene" [17].

Some comments

The idea of dynamic interacting groups of people, moving from place to place, even back-migrating if necessary, is much more exciting than the linear models so commonly found in the study of our ancestry, where admixture events were not even considered until relatively recently.

Clearly the paucity in fieldwork in Asia compared to Europe or Africa is one of the reasons for the lack of solid evidence regarding archaic remains and tools. The dating issues are perhaps complicated in Asia when compared to Africa due to soil conditions or climate.

Another factor to take into accunt is mindset; precocieved notions tend to fog the clear vision needed to identify remains or toolage as such: if you are not expecting to find tools 1.5 Mya, then you will never dig into strata of that age or older. Probably, as suggested by Dennell,[7] our australopithecine ancestors left Africa long before H. habilis (say 3 Mya), but nobody has bothered to investigate it.

Homo erectus was a versatile creature that adapted to a wide range of environments and survived for over 1.8 My. They surely admixed with modern humans (Isn't it surprising that H. erectus admixture has not yet been studied seriously - yes, there are some papers mentioning introgression with archaic "X" hominins, but not much refrence to H. erectus being "X") and perhaps were absorbed so thoroughly that they just disappeared.

Now, did they stop in China, or did they keep on marching north, into Siberia? They could cope with cold climates in North China, why would they stop there and not go on? I propose that they did, and reached America, but that is the subject of another post.

To be continued in Part 2

Sources

[1] Bar Yosef, O., Goren-Inbar, N., (1993). The Lithic Assemblage of 'Ubeidiya. A Lower Palaeolithic Site in the Jordan Valley. Institute of Archaeology, Hebrew University of Jerusalem
[2] Gaudzinski, S., (2004). Subsistence patterns of Early Pleistocene hominids in the Levant -taphonomic evidence from the 'Ubeidiya Formation (Israel)". Journal of Archaeological Science 31(1):65-75
[3] David Lordkipanidze et al., (2013). A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo. Science 18 October 2013. Vol. 342 no. 6156 pp. 326-331; doi: 10.1126/science.1238484
[4] Miriam Frankel, 28 July 2010, Notes from an excavation, News. Nature. doi:10.1038/news.2010.377
[5] Doronichev V.B., (2008). The Lower Palaeolithic in Eastern Europe and the Caucasus: A Reappraisal of the Data and New Approaches. PaleoAnthropology 107–157.
[6] Rendell, H., W. Hailwood, and R. W. Dennell. (1987) Magnetic polarity stratigraphy of Upper Siwalik Sub-Group, Soan Valley, Pakistan: implications for early human occupance of Asia. Earth and Planetary Science Letters 85:488-496.
[7] Robin Dennell and Wil Roebroeks, (2005). An Asian perspective on early human dispersal from Africa. Nature 438, 1099-1104 (22 December 2005) doi:10.1038/nature04259
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Friday, June 13, 2014

mtDNA C1 haplogroup in Europe a Post Script (The X2a hg)

A note to add to my previous post on the mtDNA C1 haplogroup in Europe, and new data regarding X2 haplogroup.

Before her 2014 paper (cited in my post on C1 hg), Der Sarkissian had studied the mtDNA sequenced from Northwestern Russian remains in her 2011 doctorate thesis [1]. Her comments were prescient because in 2014 they were classified as a new hg: C1f; she wrote: "the Uznyi Oleni Ostrov C1 haplotype may in fact represent a distinct European-specific lineage" not linked to the C1 found among Western Siberians.

This Russian C1 was described as "a genetic outlier at the periphery of its proposed origin" (in South Western Central Asia) and its "absence... in other ancient and modern-day European populations suggests that the spread of haplogroup C did not reach further west into central Europe". [1]

She underlines its antiquity when she gives the reason that this haplotype survived for so long: the isolation of this group and maybe, the "closed mating system in isolation with other Mesolithic populations of Scandinavia" [1]

But orthodoxy imposes its imprint on the thesis, and the Amerindian C1b, C1c and C1d lineages are shown as "newer" (the image below shows this clearly) than the "older" Eurasian C1e and C1f lineages from Iceland and the Uznyi Oleni Ostrov site:

Phylogenetic tree for C1 mtDNA haplogroup. From [1]

But the really interesting part is that Der Sarkissian points out that another mtDNA haplogroup X2 is very similar to the mtDNA C1 hg in that:

It is found at relatively low frequencies in contemporary populations
It has a very wide geographic range (from North America to Europe and also Siberia, the Middle East, North Africa and Central Asia)

These similarities suggest a similar evolutionary history for both X2 and C1.

Furthermore X2a (the Amerian clade) split early from the other ones; the split took place in the Middle East and from there the X2a carriers swiftly moved on into Siberia and accessed America in a second migratory wave, not long after the first wave. [2]

The X2 haplogroup

I recall reading about X2 when I was researching for my book (Monsters of Patagonia) back in 2009, and at that time thought that it was most likely due to admixture from contact with Europeans post-1492 discovery of America. This was founded on the idea that it was an Old World haplogroup and that it was only found among certain North American tribes that had been in direct contact with the French and English colonies in Canada and what would later become the US.

Furthermore I was reluctant to engage in further investigations because I found the Solutrean hypothesis as a source for the X2 mtDNA population was rather weak, and some theories regarding ancient Greek admixture into the Cherokees and other North American natives as too flimsy (I omit the Mormon theories and quack Atlanteans as totally non-scientific). There were no serious papers on these subjects and mostly posts in questionable - racist - supremacist forums made me drop further research, until now.

Encouraged by Der Srakissian's thesis I decided to look into the X2 hg once again, and came up with the following details, summarized below: [2][3][4]

Haplogroup X has a wide geographic range covering Europe, North Africa, Asia and North America
It descends from the ancient N haplogroup, dating back to at least 30 kya. It evolved from N in the Near East and surrounding areas of Western Eurasia
It is currently found at very low frequencies in Europe (less than 5% of all MtDNA)
Three populations carry it at high frequencies: Orkney Islanders (7%), Georgians 8%, Druze (11%) -The Druze have the greatest diversity of X lineages of any population X1a, X1c, X2b, X2e, X2f, X2h and X3 and their territory is very likely a refugia of the original X population [4].
It is found among Neolithic Europeans at surprisingly high rates: Elau, Germany (4,6 kya), at 22.2%, [5] and 12.5% at Calden, Germany (3000 cal BC), [6]. In these sites all carriers were X2 hg.
It is split into two clades, X1 and X2: [2]
- X1 is found in North and East Africa, with entry routes along the coasts of the Red and Mediterranean seas
- X2 spans Eurasia and is also found in North American natives (X2a haplotype)
X1 is higherst in Africa (36.8% of the X carriers there are X1)
X2 prevails in the Middle East, Europe and South Caucasus (97.2% of X hg carriers are X2) and in Central Asia and Siberia (100%)
X2a (the Amerindian clade) does not have any close relative in the Old World, including Siberia (Altaian X2e2a is another haplotype which is more recent). Was it lost due to genetic drift?
X2a split very early from all other X2 haplotypes in the Middle East, right after X began to expand at the time of the Last Glacial Maximum (LGM)
Coalescence time for X2a is 18,000 +⁄- 6,800 ya.
X2a occurs only at a 3% frequency among North American Natives, so it is quite uncommon
Its range in US and Canada is centered in the Great Lakes and the Western Plains, and has some outliers in Washington State and Arizona. Perego explains this range as caused by a central dispersion corridor from Beringia to the Great Lakes after the ice sheets receded [7]
X2a prevails among the Algonquian natives such as the Ojibwe and Chipewa (25% frequency), and is strong among other natives to the West of them: Sioux (15%), Nuu-Chah-Nulth (13%), Navajo (7%), and Yakima(5%). The presence in the Navajo (Southern Na-Dene) is most probably due to recent admixture with other northern Native Americans
It has not yet been detected in Central or South America
The American haplotypes are: [*]
♦X2a1
   - X2a1a: Sioux and Tanoan speakers
   - X2a1a1
   - X2a1b: Ojibwe people
   - X2a1b1
     - X2a1b1a
   - X2a1c: Ojibwe people
♦X2a2: Nova Scotia and Newfoundland

Comments

[*] Perhaps there is even more diversity among Amerindians: Perego [7] classified an outlier X2g, that lacked the markers of X2a1 and was different from the other Old World X2 branches, suggesting another extremely rare founder line in America.

An interesting point regarding X's antiquity is "that the basic phylogenetic structures of the [X and U] mtDNA haplogroups in West Eurasia and North Africa are as ancient as the beginning of the spread of anatomically modern humans in this region." [2], which in this paper is dated as 23 - 36 kya, close to the LGM. X is believed to have undergone "a long incubation period coinciding with and following the most recent out of Africa expansion" [4] placing it even further back in time.

Time for my wild hypothesis...

It is old, Neanderthal old. It appeared in the heart of their Eurasian realm. Its current low frequency is due to sucessive overlays of modern human mtDNAs. It was more frequent in the past as shown by the German Neolithic remains. Some refugial areas on the fringes of Europe (Orkney Islands, the Caucasus and the Druze highlands) retained a higher frequency.

The eastern Neanderthals moved on, across Asia following the animals they hunted perhaps long before the H. sapiens OOA move. These Neanderthal peopled the New World. None remained in Siberia that is why it is not found there now. They entered America along the only available corridor open to them reaching the Great Lakes area.

I checked when this corridor was open earlier than 20 kya to provide an entry date into America and came up with the Sangamonian period 125 to 75 kya [8], so it is not so far fetched.

The Neanderthals settled there (perhaps their migration followed specific prey whose range ended there). They never moved on, further South. These were cold-climate people. Later waves of migrants occupied the rest of the New World, sealing these X2a carriers off in their current range.

But... X2 is a Homo sapiens mtDNA haplogroup, not a Neanderthal one. So the theory outlined above is wrong.

Yes, if we accept current timelines for mtDNA evolution. But if we consider that the times are underestimated, that the coalescense time for X2 is not 40 kya but 150 kya and that the African Eve is not so recent, and maybe even found in Eurasia... that perhaps the coalescense leadst to a non sapiens hominin, then it could be possible to accept the scenario outlined above.

I already mentioned something similar regarding the Y chromosome evolution, and am still trying to figure out how to write a post on this subject. The main objection I find is that the real Neanderhtal mtDNA that has been sequenced until now is very different to ours and lies on a distinct phylogenetic branch. Definitively more analysis is needed before I can post on this subject!

Sources

[1] Der Sarkissian, Clio, (2011). Mitochondrial DNA in Ancient Human Populations of Europe Doctorate Thesis Univ. of Adelaide, South Australia.
[2] Maere Reidla et al., (2003). Origin and Diffusion of mtDNA Haplogroup X Am J Hum Genet. Nov 2003; 73(5): 1178–1190. Oct 20, 2003. doi: 10.1086/379380
[3] Europedia, Haplogorup X (mtDNA) www.europedia.com
[4] Shlush LI, Behar DM, Yudkovsky G, Templeton A, Hadid Y, et al., (2008). The Druze: A Population Genetic Refugium of the Near East. PLoS ONE 3(5): e2105. doi:10.1371/journal.pone.0002105
[5] Haak et al., (2008). Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age. PNAS November 25, 2008 vol. 105 no. 47 18226-18231 10.1073/pnas.0807592105
[6] Lee, E.J., et al., (2012). Collective burials among agro-pastoral societies in later Neolithic Germany: perspectives from ancient DNA. Journal of Archaeological Science.
[7] Ugo A. Perego et al., (2009). Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups. Current Biology Volume 19, Issue 1, 13 January 2009, Pages 1–8. doi: 10.1016/j.cub.2008.11.058
[8] Peter C. Lent, Muskoxen and Their Hunters: A History. pp 18