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Tracing Ancestral Origin by Haplogroups

A Workpaper In Progress by Herbert Holeman, PhD.

Notes Posted .

DNA analysis is a powerful tool for population genetics. It allows for reconstructing worldwide human diversity through distinct genealogical lineages, known as haplogroups. Such haplogroups trace human evolutionary history across populations and time periods.

In this workpaper, I trace the sequence of genetic branches in my haplogroups from tens of thousands of years ago to the present.

What allows me to do this is explained in a blog by the DNA service provider. 23andMe: "Each haplogroup describes individual branches -- or closely related groups of branches -- on the genetic family tree of all humans. All members of a haplogroup trace their ancestry back to a single individual."

For reading ease, I refer to my genetic ancestors in my workpapers as just ancestors.

A person's genome contains an evolutionary history written in DNA. It is embedded in my genome in the form of genetic mutation patterns I inherited from my very first ancient ancestors.

DNA Haplogroups relate to that inherited deep ancestry. They represent a genetic group of people who share a common ancestor on the patriline or the matriline.

Unlike traditional genealogy, tracing family connections back a few hundred years, haplogroups enable me to track my ancient roots from tens of thousands of years ago.

Through the haplogroups, revealed in my DNA tests, I have identified the deep ancestral clans to which I belong. I am able to trace the entirety of my ancestry back to a single matrilienal founder event about 43,000 years ago and similarly to a single patrilineal founder event 24,700 years ago.

To explore the origin and milieu of my ancestors, I rely on two tests: mitochondrial DNA, known as mtDNA and Y Chromosome DNA, or Y-DNA. These two tests reveal unmixed inherited genetic data in my genome.

mtDNA is inherited genetically through only my matrilineal line. That is to say it is passed to me from my mother, who received it directly from her mother via her mother's mother and so on.

The mother’s mtDNA is inherited almost identically by her offspring. From mtDNA, molecular anthropologists infer maternal lineages based on mitochondrial data of different global populations. These ancestral lineages are organized in a tree-like world mtDNA haplogroup map with each branch of the tree representing a mtDNA haplogroup with similar mutations. Prediction of my mtDNA haplogroup through comparison of my test results and the reference mtDNA haplogroup tree has enabled tracing the origin, evolution and migration history of my maternal lineage.

In essence, these direct matrilineal lineages are recorded in a woman's mitochondrial DNA and can be traced back to a common genetic ancestor. The mtDNA test is thus ancestor-specific as it traces my single matrilineal line of ethnic ancestors.

The Y chromome (Y-DNA) test works similarly. Only males have the Y The Y Chromosome, and it’s inherited almost identically between father and son. However, because of copying errors during DNA replication, roughly 2 mutations in the Y chromome occur in each generation. Even swo, tens of thousands of years may pass before such mutations result in even an incremental genetic change of any ancestral significance.

Yet, mutations allow molecular anthropologists to infer paternal lineages, which are passed from father to son. Using the Y chromosome data of different global populations, molecular anthropologists have established a tree-like Y-DNA haplogroup world map with each branch of the tree corresponding to a haplogroup where Y chromosomes contain similar mutations.

Thus, their prediction of my Y-DNA haplogroup was based on a comparison between my DNA test results and the reference Y-DNA haplogroup global tree, which allowed tracing the origin, evolution and migration history of my paternal lineage. It is passed to me from my father, who received it directly from his father via his father's father and so on. These direct patrilineal lineages are recorded in a man's Y chromosome DNA (Y-DNA) which passes biologically from father to son and can be traced back to a common genetic ancestor. The Y-DNA test is thus ancestor-specific as it traces my single patrilineal line of ethnic ancestors.

As such, both these two tests analyze Single Nucleotide Polymorphisms (SNPs) in my genome. Over the ages, SNPs mutate. With each mutation, a descendant receives a new genetic trait, which their ancestor does not have. Thereafter, all subsequent descendants will carry that mutation. A person today will likely amass a collection of SNP mutations in their genome.

Thus, geneticists can categorize people who share the same pattern of mutations into haplogroups, which can be traced through time biogeographically. In his book, Mapping Human History, Steve Olson writes, "Mutations are the words in which the story of our genetic history is written. ... Mutations in humans living today reveal where our ancestors lived, with whom they mated, and how individuals and groups are related...mutations are the pillars of modern genetics."

Accordingly, my research relies on the findings of the DNA Genographic Project that "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." (This video provides a general view of haplogroups.)

Figures 5 and 6 trace general population world haplogroup migrations. They trace the flow of maternal haplogroup migration through mutations in mtDNA and Y-DNA haplogroups.

Figure 5
mtDNA Mitochondrial Haplogroups

For close views, click on the images to enlarge the maps.

Figure 6
Y-DNA Haplogroups

Dienekes Anthropology Blog

The Biogeographical Origin of My Haplogroups

The earliest ancestral mutations in the haplogroups, B and O established the origins of my matrilineal (mtDNA) and patrilineal (Y-DNA) clans. They came into being in the landmass of Asia during the Ice Age. The geography of Asia then was not as we know it today. Then, the land on east Asia's continental shelf was above sea level and known as Sundaland. It encompassed both present day China and the then continent of Sundaland. Within Sundaland, the present day islands of Borneo, Java, Sumatra and the Malay Peninsula were dry land above sea level. Sundaland enabled peopling Southeast Asia via overland corridors connecting what are now islands in the South China Sea.

Figure 7
Continent of Sundaland

Mitochrondrial Haplogroup B

Haplogroup B is known to have existed in Asia some 50,000 years ago. Thereafter, ~43,000 years ago, a haplogroup B ancestor received a new SNP as the result of a genetic mutation. Thus, with the advent of the new SNP, a sub -branch of haplogroup B known as B4 came into being to originate my genetic matrilineal clan in the south of present day China. Over the ages, subsequent ancestors would also add additional branches. Branches of haplogroup B are found in 60% of the population of China. My B2 branch is one of the founding haplogroups in the peopling of the Americas.

Figure 8 traces my mother-line from mitochondria DNA mutations by Time to Most Recent Common Ancestor (TMRCA). The acronym,TMRCA, represents the time of origin of a genetic ancestor, expressed in years ago. Each branch of a haplogroup has its own TMRCA.

Figure 8
My Haplogroup B Genetic Branches
B4 43,000 Origin in China
B4b 34,000 People Southeast Asia
B2 15,400 People the Americas
B2c 9,700 MesoAmerica
B2c1 7,500 Mexico
B2c1d 1,150 Southeast Mexico

Based on such a sequence of mutations David Penny reports that "Highly homogeneous haplogroup B4b lineages were found in Taiwan. The B4 and B4b1 haplogroups remain today as common among populations native to Southeast Asia and among speakers of the Austronesian family of languages. The Austronesian cluster includes the present day populations from Southeast China, Myanmar (Burma), Vietnam, Cambodia, and Laos on the mainland to the islands of Taiwan, the Philippines, Brunei, Sumatra, and the Malaysian Peninsula.

Through analyses of mitochondrial DNA (mtDNA), the B4b1 mutation is especially found today among Filipinos who share a genetic affinities with the indigenous Taiwanese and populations from Southeast Asia.

As for the migration of my haplogroup B2 ancestors into the Americas, one explanation has to do with lowered sea levels during the Ice Age some ~15,100 years ago. It is thought this allowed for the above sea level crossing by the Beringia landbridge connecting Asia to the Americas (Figure 9).

Figure 9
Haplogroup B2c1 Migration

There are issues with the Beringia route scenario however. It would have been largely impassable until 12,600 years ago when vegetation and animal life emerged, says evolutionary geneticist Eske Willerslev and arcaeologist,David Meltzer. They believe shortly thereafter, ~11,000 years ago, Beringia sank under the sea ending its role as a migration overland corridor.

Even so, there is evidence the Americas already had long been peopled with human habitation in Mexico ~33,000 years ago. The study's coauthor, Mikkel Pedersen, suggests a Pacific Coast route an alternative to the Beringia land bridge as the means of earlier migrations.

Still other research considerations include a sea crossing by outrigger from southeast Asia to South America island by island.

Figure 10
Austronesian Migration
Asia to the Americas


Whatever the route to the Americas, my early B2 ancestor is one of the founding mother-lines of the indigenous peoples of the Americas. She gave rise to my B2c descendent who ultimately reached the southern tropical lowlands of Mexico where my B2c1 mother was born in the coastal gulf state of Tabasco.

Pattrilineal Haplogroup O

The Y-DNA haplogroup O, is also known by its genetic marker, O-M175, It existed in present day China some 35,000 years ago. For thousands of generations, branches of haplogroup O have remained in china to become ~90% of China's population and that of its majority population, the Han Chinese. Genetic branches of haplogroup O are spread throughout Central and Southeast Asia.

Figure 11
Haplogroup O, Marker M175

Some 24,700 years ago, my haplogroup O ancestor received a new SNP as the result of a genetic mutation. Thus, with the advent of the new SNP, the sub-branch of haplogroup O2, also known as O-M122 came into being to originate my genetic patrilineal clan in the south of China. The O-M122 Clan peopled Southeast Asia as part of the Austronesian expansion. Today, O-M122 is found in more than 50% of men in China, ~40% among Manchurian, Korean and Vietnamese men, 35% among Filipino and Malaysian men, and some 20% of Japanese males.

Figure 12
Southeast Asia Austronesian Expansion

Haplogroup Branch O-M122 has been found in almost a majority of all Amis in Taiwan, who are a group of Austronesian people living in Taiwan. Among all the inhabitants of the major Austronesian countries such as the Philippines and Malaysia, the Filipinos and Malaysians seem to be the majority possessing the Haplogroup Branch O-M122.

In my case, DNA companies report 21% of my admixture as being Taiwanese (Amis/Atayal) who are linguistically related to the Austronesian-speaking ethnic groups of the Philippines and, more broadly, Indonesia, Malaysia, and Southeast Asia islanders.

In his paper, History and Current Debates of Archaeology in Island Southeast Asia (ISEA), 2019, Hsiao-chun Hung refers to linguistic and archaeological findings in support of the Out of Taiwan Model as valid for describing the geographic spread of populations across ISEA from Taiwan.

Similarities among the Austronesian speakers of Taiwan and the Philippines and Western Indonesia have been correlated with the migratory routes inferred by phyogeography and archeology in Southeast Asia. An interesting video of How the Taiwanese Aborigines Shaped Modern Asia can be viewed here.

On going migrations between Taiwan and neighboring islands have occurred as well within the last 10,000 years from the Visayas in the southernmost islands of Luzon, and the northern and eastern coastal parts of Mindanao in the Philippines. A modern day study sample of the Philippines as recent 1900, shows an almost pure composition, very close to the modern Taiwanese South Island Gaoshan people such as the Amis and Atayal.

The sequence of my genetic ancestral haplogroup mutations is shown in Figure 13 by haplogroup marker and by Time to Most Recent Ancestor (TMRCA), which is the number of Years Ago the ancestral mutation occured.

Figure 13
My Haplogroup O Genetic Branches

Figure 13 is based on data from the International Society of Genetic Genealogists (ISOGG)as of 18 April 2020 and by the YFull Chart timeline June 2021.

SNP Mutation Genetic Marker TMRCA Matches
Haplogroup O M175 ~29,400 East Asia, formed from M9 Eurasian clan< early Siberians
O2 M122 ~24,700 362
O2a M324 ~24,000 355
O2a2 P201 ~20,257 249
O2a2b P164 ~17,005 189
O2a2b2 F996 ~13,800 31
O2a2b2a2 F706 ~10,672 22
O2a2b2a2b F15980 ~ 6,400 19
O2a2b2a2b2 AM01861 ~4,900 18
O2a2b2a2b2c BY164485 ~3,500 2
O2a2b2a2b2c1 A16139
~2,700 years 1
O2a2b2a2b2c2 A6428 >2000 2

The geneflow of my haplogroup markers, O-P201, O-M324, O-P164, et al ancestors was among the peopling of Southeast Asia from the mainland to Taiwan and the islands ~18,000 to 15,000 years ago.

By ~4,500 years ago, the whole farming and fishing communities in southern China and Taiwan were moving to the islands of Southeast Asia in a series of migrations to become the Austronesian peoples of present day.

This migration pattern is reflected in Figure 14 compiled by the FTDNA Company with a 95% level of confidence. It shows the geographical location of Y-Chromosome test-takers who match my genetic markers. The majority of the test-takers are from the present day countries of China, the Philippines, and Taiwan.

Figure 14
Y Chromosome Test-Takers Matching My Genetic Markers
FTDNA Chart as of 16 January 2020


Some 30,000 - 40,000 years ago my ancient maternal and paternal genetic clans had their beginnings in the central East Asian heartland of the Yangtze River Basin. Over the ages, their descendants would migrate to Southeast Asia.

The vast area depicted in the Out of Taiwan Model is of interest to my biogeographical ancestral search.

They would arrive in Taiwan about 5,000 years ago and then by sea reach the Philippines a thousand years later. Thereafter, my matrilineal line reached the Americas either traveling northwest overland or by sailing westward island by island.

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