In a reply to a comment posted by a reader yesterday, I ratified my belief that the impact of the contact between Europeans and Native Americans was devastating for the latter. I have posted about this in the past:
"These studies overlook a unique situation which did not occur in other parts of the Old World: European discovery and conquest after 1492 AD provoked a massive eradication of native populations. This decreased the Amerindian gene pools dramatically (to between 33% and 4% of their original sizes). Over 80 M people died due to war and, mostly, microbia (measles, influenza, smallpox). Selective pressure acted to favor those better equipped to face the new environment.
It was this combination of disease and war-caused bottleneck plus natural selection that distorted the pre-Hispanic gene-frequency distribution obliterating genetic lineages, and obscuring ancestral frequency patterns. The pre-Hispanic genetic map of America was different and may have been much richer (i.e. similar to that of Asia or Austronesia). Studies that analyze gene frequencies in the New World do not seem to bear this in mind"
Of course, I never actually did some deeper research into the matter or looked into its genetic implications from a solid scientific point of view, although in other posts I have mentioned time and time again that the real bottleneck in Amerindian popultions took place after the discovery of America, and that it wiped out complete lineages.
Today's post will substantiate my claims that the diseases and war between natives and European conquerors led to a vast loss of genetic diversity in the Americas.
Massive death toll
Here in Argentina, during our school days they teach us about the Pre-Hispanic period in detail. We learn about the native cultures of Argentina and the Peruvian and Mesoamerican civilizations. We are later taught about Columbus and his voyages of discovery and the later conquest of America by Cortez, Pizarro, Valdivia and similar individuals. We learn about the Colonial institutions, the Viceroyalties, and the political and social aspects of colonial life. The gory details of death and the atrocities of conquest and subjugation are not mentioned.
But those students eager to read more about this period learn about the wars that took place between Spaniards and natives between 1492 and 1810. The use of cavalry, gunpowder, fire arms and war dogs gave the Spaniards a great advantage over the native troops who ony had bows and arrows, darts, spears and maces to fight the Europeans.
To make matters worse, the Spanish were aided by disease (flu and smallpox) which ran wild among the natives, decimating them.
The image above shows native Mexicans infected with smallpox, an Old World disease for which Americans had no immunity. The image is from the Florentine Codex prepared by a Franciscan friar, Bernardo de Sahagún during the 1500s. Its original title was "La Historia Universal de las Cosas de Nueva España", that is: "the Universal History of the Things of New Spain" (Mexico).
A little known fact is that Hern´ Cortez defeatied the Mexican Aztecs at their capital city of Tenochtitlan in 1520 while the natives were dying by the thousands, infected with smallpox they had caught from the Spaniards!
The Spanish knew the devastating effects of smallpox on the Indians. It had destroyed the natives in the Caribbean islands during the first phases of discovery. For instance the epidemic of 1518 in the Caribbean was terrible: "There occurred an epidemic of smallpox so virulent that it left Hispaniola, Puerto Rico, Jamaica and cuba desolated of Indians" . This actually was the reason that slaves were brought from Africa to work in the fields, there were no more natives available: The local Taino aboriginals declined from over 1 million to less than 1,000 individuals by 1550.
War against the Aztec or Inca was, however quite limited. The other native societies offered more resistance. The Maya had no central government which if taken would lead to a total surrender as happened in Mexico or Peru. They had to be taken a village at a time. They were subdued by 1697.
Even minor civilizations were problematic: for instance, the Mapuche in Chile. They engaged the Spaniards and, in 1536, just after they arrived, torching the recently founded town of Santiago (which nowadays is the capital city of Chile). The Spaniards held firmly on and pushed the Mapuche south, into the Chilean Lake District. War raged on for years but the Spaniards managed to settle the Lake District in the 1560s, after defeating the native chief Caupolicán (1558) and impaling him.
The Araucanian or Arauco wars simmered on and the towns of Villarica, Osorno, Angol, La Imperial, were razed in 1598. The Spanish government retreated north and consolidated their frontier along the Bío Bío River. Native raids and uprisings led to a negotiation in the mid 1640s which concluded in an uneasy truce that lasted from 1665 to the 1860s.
In northwestern Argentina, the Kakán natives or Diaguita that lived in the fertile river valleys of the Andean foothills resisted Spanish occupation for over a century: the "Calchaquí Wars".
The area nowadays is a tourist attraction traversed by Argentina's National Highway Ruta 40, with cacti, arid mountains towering over 6,000 m (19,700 ft.) and the highest vineyards in the whole world, but the hundreds of "antigales" or ruins of native villages attest to a violent past.
Among the ruins is the settlement of the Kilmes or Quilmes natives. They lived by the Calchaqui River valley in Tucuman province, Argentina and firmly resisted the Spanish invaders. They held out in their mountain fortress against the Spaniards for decades during the Calchaqui Wars (1560 - 1666) but were defeated in an unexpected mid-winter raid in which the Spanish were aided by a traitorous group of neighboring natives.
Their village was destroyed, and the natives were transplanted en masse to Buenos Aires and forced to walk there (1,200 km or 746 mi.). Hundreds died on the way. They were "reducido" (restrained) in what is now a suburb of Buenos Aires, that adopted their name: the town of Quilmes. Finally, in 1812 the remaining three descendants of the Kilmes were set free.
The Kakan or Diaguita language is lost, nobody speaks it, it survives in place names recorded by the Spaniards in the 1500s, but the meaning is mostly unknown.
Other regions were left untouched by Spanish troops, but the European disease reached them (Amazon, Chacoans, Patagonian natives).
The European presence weakened the locals in many ways: the domestic animals that they introduced brought new diseases with them that infected the natives (tapeworm for instance). The natives were forced to leave their traditional villages and were gathered in other more densely and unhealthy towns built by the Spaniards. Lack of hygene and overcrowding soon promoted the spread of diseases (cholera and TB). Even the quality of the food intake fell. Less animal protein and more carbohydrates were ingested by the natives. Children were undernourished and tooth decay increased.
American Colonies and British bio-warfare in the 1700s
Even the North American colonies used terrible weapons against the natives. The English Commander officer during the French and Indian War (1754-1763), Lord Jeffrey Amherst, considered the natives' lives worthless and believed that they should be exterminated. He arranged for blankets infected with smallpox be sent to the natives to spread disease among them . He was a pioneer in bio-warfare, using lethal (for the Indians) germs as a weapon.
After the Independence wars, the young American nations advanced their frontiers and soon the whole continent was under the control of Western people. I will not delve in the US opening the West or the Chaco and Patagonian wars of Argentina and Chile. Those were military campaigns with clear goals, and they did not intend to deliberately destroy civilians, only subdue them to the central governments.
Post-Colonial Genocide 1850 - 1900
Devastation continued once the colonial period had finished. The well intended Anglican Missionaries in Tierra del Fuego set out to civilize the Yamana (or Yaghan) canoe people living there. The natives had managed to adapt to the harsh Fuegian environment for over 6,000 years, but the American and European whalers of the mid 1800s wiped out the sea mammals that they hunted. Starvation began the process of extinction.
Mingling with the whalers put these formerly isolated natives in contact with tuberculosis, smallpox, tifus, whooping cough and measles. From a population of over 3,000 in 1850, the natives which had gathered at the Mission in Ushuaia (known by the natives as "welapatux-waia" or "Bay of death"), dropped dramatically. By 1900 their culture had vanished. By 1995 only 74 persons state that they have a Yamana ancestry.
The consequences from a genetic perspective
The dreadful impact of discovery and conquest can be imagined just by looking at the death toll: "the American Indians were at least seventy million or maybe more when the foreigners showed up on the horizon. One and a half centuries later, they were reduced to only three and half million". 
That is one incredibly big bottleneck: only 1 out of 20 natives survived. This means that 95% of the genetic diversity of America died out. Perhaps the real figure is not 95% (below we will see a paper mentioning a 50% drop) , but still, it is clear that what is left today is just a pale shadow of the diversity that once existed in America.
Death and decreasing diversity
Disease and War cause extreme reduction in population sizes and this impacts noticeably on its genetic diversity . In Europe, the Black Death or plague in 1347-1351 caused a very high death toll (between 30 and 50% of the population died) , and the effects of this disease-caused bottleneck are even visible in the current genetic diversity of Britons: 
A paper  shows a dramatic decrease in Diversity as measured by haplotypes ⁄ sampled individuals:
- 0.84: Saxon Britain
- 0.75: Ancient Britain
- 0.45: Modern England
In other words currently 53% (0.45⁄0.84) of the former genetic diversity survives, 47% was lost.
See Table 1 in  for a full set of data showing a considerable drop in genetic diversity. The finding surprised the authors: "Based on the assumption that modern England is more cosmopolitan, higher geneitc diversity in the ancient sample was unexpected" . And the reason for this was the bottleneck caused by the Black Death and the Great Plague of 1665 - 1666 (which wiped out 20% of the population of London).
The paper's comments regarding the impact of a disease on diversity are also valid for America, though we can imagine an even more drastic effect among the Amerindians due to the severity of their bottleneck:
"Because most human haplotypes are rare, lineages could have been forced to extinction even without a severe population bottleneck (millions remained). This is especially true if related families were lost when whole villages perished (either through shared susceptibility or environment). Furthermore, during the plagues some families were apparently more resistant than others, which could have led to high variance in the number of daughters surviving among different families and a consequent loss of mtDNA diversity at the population level. 
The upheaval caused by disease also favored some haplotypes more than others: an ancient haploytpe known as the Cambridge reference sequence (CRS) was found at 6.3% frequencies in the ancients but subsequently grew to almost 22% among modern Britons. 
A Native American study
So if this is what a mere 33 - 50% reduction in population caused in Europe, imagine Amerindians, whose population fell by 50 - 95%!
A very interesting paper by Brendan D. O'Fallon and Lars Fehren-Schmitz, (2011)  addresses the genetic impact of European contact in Native Americans. They are more cautious in their population decrease figures, but even so the value they estimate is very high: "Native Americans suffered a significant, although transient, contraction in population size some 500 y before the present, during which female effective size was reduced by ~50%" from the maximum it had reached about 5 ky BP. 
The authors compared ancient (3,000 BC to 1,200 C.E.) mtDNA and modern samples from North and South America to study how the population bottleneck impacted on diversity. They found that it "affected haplogroups C and D disproportionately" (D1 was hit worse than C or A2, B2 and X2a), and that "the depopulation was not localized to particular regions or communities, and instead, was likely to have been widespread... [and] had an especially severe impact on the most populous regions." 
Figure 4. in the paper, shown below clearly marks the "lost" haplotypes: "blue" in South America, "red" in North America, while gray represents the extant lineages.
It is interesting to see that most of the "lost" branches don't have any descent today they simply disappeared (it is not the case of a four pronged fork where 3 prongs died but one survived, in these lineages all prongs went extinct9.
The ancient samples they used came from 16 sites which is quite a lot, but they originated in only three geographic locations: SW Ontario, Canada; Fulton County, Illinois US and Palpa, Peru. Imagine if more locations from across America are added, will new haplogroups be found? I believe so.
For instance, take haplogroup M, which has not been found in any contemporary Native American group but has been reported at least twice in ancient remains (see my post on Ancient migrants into America with Hg M) and another recent study (Carpenter et al., 212)  which found mtDNA belonging halpogroup in pre-Columbian Chachapoyan and Chachapoya-Inca remains dated at 1,000 and 1,500 AD. They came from the Laguna de ls Cóndores site in Peru.
So, having said this and looking at the tree above I imagine that much more diversity was much more ample than we can imagine and that haplogroups other than M may have also existed in America and got lost in the discovery debacle.
 From Gerónimo de Bibar Crónica y relación copiosa y verdadera de los reynos de Chile
 Lord Jeffrey1 Amherst's letters discussing germ warfare against American Indians. www.nativeweb.org.
 Oviedo y Valdes G. F. (1851-1855), Historia General y Natuarl de las Indias..., Vol 1. 105.
 Bernardo Veksler, Una Visión Crítica de la conquista de America  A.L Töpf, M.T.P Gilbert, R.C Fleischer and A.R Hoelzel, (2007). Ancient human mtDNA genotypes from England reveal lost variation over the last millennium. Biol Lett. Oct 22, 2007; 3(5): 550–553. doi: 10.1098/rsbl.2007.0269
 Montgomery Slatkin, (2004). A Population-Genetic Test of Founder Effects and Implications for Ashkenazi Jewish Diseases. Am J Hum Genet. Aug 2004; 75(2): 282–293. doi: 10.1086/423146
 Brendan D. O'Fallon and Lars Fehren-Schmitz, (2011). Native Americans experienced a strong population bottleneck coincident with European contact. Pnas 20444–20448, doi: 10.1073/pnas.1112563108
 Meredith L. Carpenter, et al., (2013). Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. Am J Hum Genet. Nov 7, 2013; 93(5): 852–864. Table S1. doi: 10.1016/j.ajhg.2013.10.002
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