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

Sunday, March 29, 2015

On the bottleneck of Males 8 kya (Karmin et al.)

A paper (A recent bottleneck of Y chromosome diversity coincides with a global change in culture, (2015) Monika Karmin et al. Published in Advance March 13, 2015, doi:10.1101/gr.186684.114 Genome Res. 2015.) suggests that the evolution of farming reduced the number of reproducing males to a minimum, and thus created a bottleneck in Y chromosome diversity as many male lineages became extinct as they could not pass on their genes (and Y chromosomes) to the next generation.

The idea is that as humans became sedentary some 10 kya, some males became dominant and accumulated wealth, power and, as expected, this gave them access to the women and excluded the other less "fit" males. The ratio reported for that period is as many as 17 women reproducing for every one man who passed on his genes.

The paper is paywalled, but the Supplementary Material is free. So I peeked at it and was surprised by the following figure (S4B):

Fig. S4B from Karmin et al..

Yes, All populations (But one) see a dip in the effective population size between 10 and 3 kya., followed by a rebound and growth. The only group to show another trend: Andean natives, whose population just steadily declines from 3 kya onwards.

First let's read the Abstract:

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

But let's not forget that the analysis is based on saliva swabs taken from extant males around the world and the genetic data was then subjected to statistical processing which yielded an evolution of the reproductive populations both male and female.

In other words we are "guessing" how the diversity of Y chromosomes evolved over time in different regions. It is not like they sampled ancient remains and did a direct measurement. This is again, a conjecture based on statistic inferences.

In other posts I have expressed my doubts regarding these methods. Here I express them again.

The "Andeans" that were surveyed were Colla (or Kolla) who inhabit what is now Bolivia and Peru, and raised llama and alpaca camelids and grew crops of corn, potatoes, peppers, squash, tomatoes, cotton, quinoa among others. The other "Andean" group actually lived in the Chaco savanna region, a flat area that lies to the North of Argentina. They grew squash, melon.

What made these people so different from the rest of humans? An explanation is needed.

Maybe the whole dip is just a statistical artifact.

But assuming it is real. Are we to expect that the development of farming (something so labour intensive) would lead to some males prevailing over others and inseminating all available women?

Can we imagine a primitive farmer society with men gathering on average 17 women each, in harems and, obviously dispossessing the other 16 males of women with which to mate with?

How about a world that just became sedentary, with higher ratios of diseases associated to sedentary life, with naturally weaker males dying in their childhood, or later during their teens and early adulthood in inter-tribal warfare? Women, subjected to plunder and rape by the victors would bear the children of the new dominant groups while the other men became slaves with no reproductive rights...

Are we to imagine that Wichi and Colla in South America were less warlike people? or had some other tendencies?

I don't think so, and propose an alternate explanation (admitting that it is not a statistical artifact). It is very unlikely, but somehow explains the bias against men and the drop of diversity... As I wrote in my post on Neanderthal - Human admixture:

Haldane’s law [2] which states that:
When in the offspring of two different animal species one sex is absent, rare or sterile, that sex is the heterozygous sex
Heterozygous sex meaning the offspring with two different sex chromosomes: XY, that is, the male. In plain english Haldane is saying that a male (Neanderthal) and a female (Homo sapiens) would have had more daughters than sons (boys would be rare). These few, if any (absent) boys would be carrying their Neanderthal father’s Y (Neanderthal) chromosome and, they would be very probably sterile and therefore did not have children and could not pass on their Y chromosome to their sons.

In other words, humans and Neanderthals mixed and the male Neanderthals passed on Their Y to boys who were sterile and therefore the Y diversity was reduced (every Neanderthal mating was one less human one)...

What about the Andeans... their slump came later and continued... were there relict Neanderthals in America? By the way, look at the curves of the Central Asians and Africans, they dropped and actually, never recovered while the others did. Would this reflect a later admixture in those locations?

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Wednesday, March 25, 2015

Neanderthals, Psoriasis and Native Americans... a Link

A very interesting paper by Yen-Lung Lin, Pavlos Pavlidis, Emre Karakoc, Jerry Ajay, and Omer Gokcumen, " Variants Shared with Archaic Hominin Genomes" takes a look at "polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed)...", some of these deletions are the cause of well known diseases.

I decided to see if there were any hints at a link between Native Americans and diseases prevalent among Neanderthals and this is what I found:

The previous paper by the same team (The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes by Yen-Lung Lin, Pavlos Pavlidis, Emre Karakoc, Jerry Ajay, and Omer Gokcum. Mol. Biol. Evol. doi:10.1093/molbev/msu405 Advance Access publication January 2, 2015) states that one of the deleted sequences shared by humans and Neanderthals is the LCE3C gene deletion: "...which has been strongly associated with psoriasis (de Cid et al. 2009). The allele frequency of LCE3C gene deletion is extremely high among Eurasians, reaching to over 70% allele frequency in some European and Asian populations..." it is the authors' "understanding that this deletion has been maintained in high allele frequencies since before Human– Neandertal divergence."

So According to this study, the genetic risk factor that causes psoriasis has been in our family tree for some 500,000 years. It was carried by our ancestors and the ancestors of Neandertals and Denisovans too. In fact, it was carried by our common ancestor.

The interesting part is that it prevails among Eurasians... But what about our African ancestors. Do they have it in high proportion too as would be expected from this genetic variant that appeared before humans and Neandertals split?

Lets see what variant of the psoriasis risk gene is found in Africa: The paper Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders, by Laia Bassaganyas et al. (2013) BMC Genomics 2013, 14:261 doi:10.1186/1471-2164-14-261. Gives us some data:

This paper finds that "...most populations tend to have a higher frequency of the deleted allele than Sub-Saharan Africans." Which at first sight means that Africa, the land where the deletion is supposed to have appeared 500 kya, now has a lower prevalence of it. Surprising and unexpected.

The paper adds that "The deleted allele (LCE3C_LCE3B-del) is common in patients with psoriasis among populations of European ancestry, and in Chinese and Mongolian populations", ratifying what Lin et al mention in their study. Furthermore, Bassaganyas found that "Populations from Eastern-Asia, America and Oceania had greater differences in signal intensity with respect to the YRI (Yoruba) population than other Sub-Saharan African, European, Northern African and Middle East populations, as well as more copy-number variable regions...". So East Asians, Africans and Oceanians are the most distinct when compared to Africans.

But there is more: Amerindians are, once again among them most different. "The aCGH data for the LCE3C_LCE3B-del showed lower intensity values for all the studied populations respect to YRI, and five of them (Pima (PIMA), Brahui (BRA), Mozabite (ALG), Maya (MAYA) and Chinese Han (CHB)) presented log2 ratios ≤0.25, limit considered significantly low for a copy-number loss ..."; these groups are Maya, Pima (America), Brahui (India), Chinese and Mozabite (North Africa).

These are the deletion ratios found by Bassaganyas et al: (bold mine)

The highest frequency of the deletion was detected in the PIMA population, with an allele deletion frequency of 75% (log2 ratio in the sample pool of −0.67). The ALG population also had a high frequency of the LCE3C_LCE3B-del (67% with an intensity log2 ratio of −0.30). As expected from the aCGH data, Sub-Saharan populations have low frequencies of the deleted allele (28% in Bantu (BAN), 34% in YRI, and 35% in Pygmies (PYG)). However, two Asian populations (Hazara (HAZ) and Yakut (YAK)) have a LCE3C_LCE3B-del frequency lower than that of Sub-Saharan Africans (21% in HAZ and 23% in YAK), although the small number of samples for these two population groups (17 and 11 samples) made the estimation of their low frequency unreliable. The frequency of the LCE3C_LCE3B-del in the other populations varied between 50% and 62%.

I find it interesting that the Central Siberian Yakut have an even lower deletion frequency than Africans do. Because the Yakuts are supposedly realted to the source of Native Americans. They would be expected to have a high deletion frequency. Instead, theirs is among the lowest.

The authors then took a look at the genotype frequencies for the LCE3C_LCE3B CNV and found that the most common variant in all populations isthe heterozygous state. The Sub-Saharian Africans have the non-deletion homozygous state at higher frequencies (which they share with some curious outliers: the Karitiana Native Americans, Italians and Yakults). The rest of non-Sub-Saharians have higer frequencies of the deletion homozygous state.

There is a clear Sub-Saharian vs. Rest of the World cut. But why woudl Yakults and Karitiana share this feature with Africans?

An explanation is: those groups provided small sample sets, and they are isolated from other people and therefore less admixed with others and with a higher inbreeding ratio. Genetic drift and restricted gene flow led to the current pattern of global distriburion, where the result of genetic drift or recent selective pressure.

However Lin et al. suggest that these deletions have been with us for half a million years and despite causing psoriasis (as well as lupus and reumatoid arthritis),they have resisted selection against them.

Bassaganyas' team notes that this deletion behaves differently to other genetic traits: "While the trend observed for general LD consists of a successive increase in the LD in Middle East-North Africa, Central South Asia, Europe, East Asia, Oceania and America with respect to Sub-Saharan Africa, we essentially detect low r2 values in African populations and similar high values for the rest of the world." In other words it is not the typical bottleneck of an Out of Africa migration.

I did expect the "founder effect" and "bottleneck" explanations, and it is clear that Psoriasis is high out of Africa, as would be expected by the higher deletion frequency outside that continent.

If the ancestor of Neanderthals, Denisovans and Modern Humans carried the deletion and in turn we all carried it too, why is it so much lower in Africa? Why would other groups keep it while Sub Saharian Africans lost it? Can we imagine a scenario that explains this?.... Yes:

Lets imagine a more distant human relative like H. erectus, carrying the deletion, which gave it an adaptative advantage in its conquest of Eurasia. Erectus' descent, Neanderthals, Denisovans and us, carried this deletion of Asian origin. Some back migration into Africa took the deletion there too, where its lower frequency reflects less introgression and a recent admixture. Older populations with the deletion have it at higher frequencies, and those who peopled America have it at highest ratios. It is clear that its adaptative advantages were handy when conquering the New World too.

Later Out of Africa humans mixed with the Eurasians and watered down the deletion with a west to east cline. Maybe the Yakuts aand Italians have a higher frequency of African input. The Karitiana too... slaves escaped from Brazilian plantations into the Amazonian jungles....

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Neanderthal demise due to a volcanic eruption 40kya?

A paper published on March 19, 2015 (Campanian Ignimbrite volcanism, climate, and the final decline of the Neanderthals, by Benjamin A. Black, Ryan R. Neely and Michael Manga in Geology doi: 10.1130/G36514.1) proposes that a volcanic eruption 40 kya gave the final coup de grace or death blow to a declining Neanderthal population in the northern parts of Eurasia:

The eruption of the Campanian Ignimbrite at ca. 40 ka coincided with the final decline of Neanderthals in Europe. Environmental stress associated with the eruption of the Campanian Ignimbrite has been invoked as a potential driver for this extinction as well as broader upheaval in Paleolithic societies. To test the climatic importance of the Campanian eruption, we used a three-dimensional sectional aerosol model to simulate the global aerosol cloud after release of 50 Tg and 200 Tg SO2. We coupled aerosol properties to a comprehensive earth system model under last glacial conditions. We find that peak cooling and acid deposition lasted one to two years and that the most intense cooling sidestepped hominin population centers in Western Europe. We conclude that the environmental effects of the Campanian Ignimbrite eruption alone were insufficient to explain the ultimate demise of Neanderthals in Europe. Nonetheless, significant volcanic cooling during the years immediately following the eruption could have impacted the viability of already precarious populations and influenced many aspects of daily life for Neanderthals and anatomically modern humans.

The paywall protected paper indicates that the drop in temperature impacted negatively on the Neanderthals (makes one wonder what happened to Modern Humans who lived in those same regions... why would a 3 to 9°C temperature drop hit one group but not the other? Furhtermore, the dip in temperatures seems to have been worse in lower latitudes i.e. ASEAN, China in comparison to Western Europe...

Volcanic winter

Photo : B.A. Black et al. and the journal Geology) Pictured: Annually averaged temperature anomalies in excess of 3 degrees Celsius for the first year after the CI eruption, compared with spatial distribution of hominin sites with radiocarbon ages close to that of the eruption.

Anyway they focus on the European Neanderthals but what about those in Asia? South of central North America (current USA) the temperature drop had no impact, so any New World Neanderthals living in the Midwest or south of it would have faced no serious consequences due to the "volcanic winter".

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Tuesday, March 17, 2015

Yeti is not a polar bear... it is a brown one

Over a year ago I posted about a paper that proved that Yeti and Polar Bears were related. But now another paper seems to disprove the original paper: Gutiérrez EE, Pine RH (2015). No need to replace an “anomalous” primate (Primates) with an “anomalous” bear (Carnivora, Ursidae). ZooKeys 487: 141-154. doi: 10.3897/zookeys.487.9176. The new paper says that: "We have concluded that there is no reason to believe that the two samples came from anything other than Brown Bears." In other words, bears that DO live in the region.

The point is: how could have bears fooled local folk into believing that the hairs were of a strange primate?

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 
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