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Haplogroups and Ancestral Origin

A Work In Progress by Herbert Holeman, PhD.

This draft workpaper was last modified .

Findings to date

• My maternal haplogroup is B, which extends from a woman in Asia 43,000 years ago to population subclades in present-day Latin America and Mexico.

• My paternal haplogroup is O, which stems from a man ~30,000 years ago in China with population subclades remaining in Southeast Asia.

• My genetic ancestors interacted with other ancient hominids, and I share traces in my DNA of 1.4% Neanderthal and 1.8% Denisovan.

• My ancestors' migratory routes were expanded by the existence of the continent of Sundaland and the Beringia Land Bridge, which allowed my maternal ancestor to migrate from Asia into the Americas.

• Genetic flow from 40,000 years old Tianyuan Man to present day East Asian Han and Ami lineages as well as to the Americas is reflective of my present genetic composition.


To depict the haplogroups unique to my genetic ancestral with a bit of milieu, I make use of haplogroups, which classify humans into ancient family clans. The distributions of haplogroups follow historical population movements and yield a historical understanding of our ancestors' history. Much like a flow chart, it traces my ancestors' geographic origin and reveals evidence of their admixture.

Depicting a haplogroup in this manner is a convenient way to view maternal and paternal ancestry through time and geographical location. The alphabetic sequence of letters assigned to name a maternal or paternal haplogroups have no relation to each other. This video explains haplogroups.

Figure 5 depicts the maternal (mtDNA) haplogroups, and Figure 6 illustrates paternal (Y-DNA) haplogroups. My mtDNA haplogroup is B, and my Y-DNA paternal haplogroup is O

Figure 5
Mitochondrial Haplogroups

Figure 6
Human Migrations and Paternal Haplogroups

My genetic history stems from these two ancestral haplogroups. Within them are genetic populations, each of which shares a common ancestor. That is to say, a common ancestor being a person from whom are descended. The concept is, "All people alive today belong to distinct haplogroups of people belonging to the same haplogroup and can trace their descent to a common ancestor and even a specific place where that ancestor may have lived." Both haplogroup B and haplogroup O originated in southern China and Southeast Asia.

Haplogroup B, which is discussed in greater detail in the workpage on Mitochondrial Full Sequence Analysis, reveals my maternal ancestry. It stems from the woman who gave rise to the haplogroup B4b woman in mainland Asia 34,000 years ago. Living as foragers, her descendants carried the line to a B4b1 mutation in Southeast Asia. More specifically, this is the haplogroup subclade that is phylogenetically closest to the American B2 haplogroup. My maternal B4b1 ancestor is found mainly in populations of southern China and Southeast Asia.

Y-Chromosome Next Generation Sequencing reveals my paternal genetic ancestry stems from the ancestor in Southeast Asia ~30,000 years ago. He gave rise to the haplogroup O2 ancestor, which is present-day China. For thousands of generations, his descendants remained to become the majority of the Han Chinese. Moreover, the O haplogroup expanded into the Philippines, from Taiwan and with the Austronesian expansion into Island Southeast Asia (ISEA). By definition, ISEA extends from Taiwan in the north and continues southward through the Philippines, Island Malaysia (including Sarawak and Sabah of Eastern Malaysia, plus Brunei), Indonesia, and East Timor.

As shown in figures 5 and 6, haplogroups are geographically specific to continents, such as Africa, Europe, and Asia. And, within each haplogroup is a unique genetic mutation pattern of Single Nucleotide Polymorphisms called SNPs (pronounced "snips"). SNPs are in a peeople's DNA. SNPs are the pillars of modern genetics and reflect small changes in the DNA, which occur naturally over time. When a SNP occurs, it passes a unique lineage marker to future generations.

People who have descended from the same ancient family clan will share the same pattern of SNPs. By looking at this pattern in present-day populations, geneticists trace backward in both time and space. They reconstruct genetic and migration lineage and map ancestral migration routes, such as that of my ancestors.

Steve Olson explains this process in his book Mapping Human History, "Mutations in humans living today reveal where our ancestors lived, with whom they mated, and how individuals and groups are related. Mutations are the words in which the story of our genetic history is written."

For research purposes, my genetic history begins in the time and place of my concluding ancestral haplogroups, formed in Stone Age communal society during the migration of modern humans into Eastern Asia in the Last Ice Age.

It was a glacial environment with thick year-round ice sheets, frigid climate, and dwindling hunting and foraging spaces. Wrapped in animal skin to keep warm in the cold environment, they sought shelter in the warmth of caves and stayed near the cave's mouth which would be lighter for better vision. Where no caves existed, they built temporary shelters from branches, leaves, and animal skins.

They made crude tools and weapons from stone and bone, stone axes, and carved wooden spears for hunting and fishing, which they cooked over a fire as hunters and gatherers. They also gathered edible plants, fruit, and collected eggs from bird nests. A single kill of a woolly mammoth would provide a clan with food for months.

With lower ice-age sea levels, Sundaland's then-existing landmass opened up corridors into Southeast Asia, now known as Taiwan, the Philippines, Malaysia, and Indonesia.

Figure 7
Continent of Sundaland

In terms of cultural evolution, no doubt, my Stone Age genetic ancestors lived among the first people in Asia to leave behind works of art. They used combinations of minerals, ochres, burned bone meal, and charcoal mixed into water, blood, animal fats, and tree saps to fetch humans, animals, and signs. They also carved small figurines from stones, clay, bones, and antlers.

Both my maternal and paternal ancestral haplogroups date back to when Tianyuan Man lived ~40,000 years ago. He was not a direct ancestor, but rather a distant cousin, of a founding population in Asia that gave rise to present-day Asians, according to paleogeneticist, Qiaomei Fu. Extracted DNA from Tianyuan Man's thighbone reveals that he is most closely related to living people in east Asia. It encompasses China, Japan, the Koreas, and Southeast Asia, including Papua New Guinea and Australia.

Interestingly, Tianyuan Man's genetic similarity to some South Americans suggests early Asian population structure. He shares much DNA with ancient and present-day East and Southeast Asians, as well as with ancient and present-day Native Americans. Paleogeneticist Erik Trinkaus says, "populations moved around a lot and intermixed." For example, the genetic flow from Tianyuan Man to present-day East Asian Han and Ami lineages as well as to the Americas, which reflects my present genetic composition. To quote from a review of the study in Current Biology, the "Tianyuan individual is related to an ancestral group that contributed to all more recent populations with Asian ancestry."

Figure 8
Genetic Similarities of Tianyuan Man

From such skeleton remains of prehistoric Asians, researchers are studying cultural patterns, lifestyles, and individual mobility of my prehistoric ancestors.

It was a time when hominids interacted with my early ancestors. Their world included living among other types of human beings relevant to my genome. At some point, my genetic ancestors encountered these other archaic humans and not unexpectedly interacted with them. Both Neanderthal and Denisovan DNA markers are present in modern Asian populations, including mine. My genome includes 1.4% Neanderthal and 1.8% Denisovan.

ISEA has been among the world's most significant passageways of human migrations since more than one million years ago, including hominids such as Homo erectus and other species of the Homo Genus, as Homo floresiensis and Denisovans.

Homo sapiens are estimated to have migrated into ISEA between 100,000 and 50,000 years ago. Several sites of ancient remains of Homo sapiens in ISEA include a find in Luzon dated 66,700 years ago and a find in Malaysia dated some 40,000 years ago. Ancient DNA suggests admixture between archaic hominins, as evidenced by the presence of Denisovan DNA in my genome.

Figure 9
Neanderthal-Denisovan Hominids

Neandertal-Denisovan image

Early on, biologist Colin Groves proposed different species of humans lived in cohabitation. And, the fact is, Neanderthals and other humanids, such as the Denisovans, had long interbred with Asians as noted in this video. Denisovans wandered Asia for hundreds of thousands of years. They remained in existence as recently as the time of my ancestors. Their genes remain in modern East Asian populations and the Oceanic islands. Records show Denisovans interbred with early modern humans in Southeast Asia, particularly among the present-day population of the Philippines. Mike Luoma points out, "As a result of ancient interbreeding, people living today on islands of Southeast Asia and Oceania have genomes with up to 6 percent. Denisovan DNA." I have 1.8% and it is relatively undetected elsewhere in the world.

Clare Wilson reports, "Our species may have been interbreeding with Denisovans as recently as 15,000 years ago." Moreover, the genetic analysis uncovered a direct descendant of two different early humans groups with the now proven existence of humans with a Neanderthal mother and a Denisovan father. This video depicts other hominids living alongside Neanderthals and Denisovans in Southeast Asia

A research team led by David Reich discovered at least three significant waves of human migration into South Asia over the past 50,000 years. During that time, the anatomically modern hunter-gatherers in Southeast Asia interacted with the ancient human Homo erectus, Homo floresiensis, and Denisovan " populations.

Besides Homo floresiensis in Flores, Indonesia, (Figure 10) other hominids lived in the area as well, such as in present-day Luzon in the Philippines (Homo luzonensis). Evidence reveals Hoabinhian hunter -gatherers occupied southeast Asia until about 4000 years ago. Both Hoabinhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity.

The National Geographic report of a study concludes that Denisovans co-existed and mixed with modern humans in Southeast Asia as recently as 15,000 years ago. The study's co-author, Murray Cox, says of the Philippines, Malaysia, etc. "Suddenly, it's kind of crystalized that the center of diversity for archaic populations is in Islands Southeast Asia."

Figure 10
Finding Homo luzonensis

Copyright © 2018 Herbert P. Holeman, Ph.D. All Rights Reserved.