Tracking migration with mitochondrial and Y chromosome DNA

Wherever we go, we bring along traces of where we have been. In genetic and genomic terms, this is the process of migration, the leaving of one population and the joining of another, either because of physical movements or because of changes in the reproductive structure of the population. All parts of the genome can now be used to track migration, but some of the earliest evidence about human history and human migration came from two specific components—mitochondrial DNA and the Y chromosome. There is an extensive literature, both in scientific journals and in popular books, about reconstructing human history using mitochondrial DNA and the Y chromosome, which we introduce here only as a brief overview.

Mitochondrial DNA—are you my mother?

Recall from Chapter 3 that mitochondria have their own genomes. The genomes of mitochondria do not mix or recombine with the nuclear genome, and the rate of mutation in the mitochondrial genome is about ten times higher than in the nuclear genome. In addition, since a cell has hundreds, or even thousands, of copies of mitochondria, all with the same genome, it proved easy to isolate and analyze an individual’s mitochondrial DNA at a time when the analysis of chromosomal DNA was far less straightforward. Furthermore, because the mitochondrial genome is relatively small—only about 16,600 bp in humans and other mammals—it was easier to work with than chromosomal DNA. Thus, studies about human migration using the mitochondrial genome began in the early 1980s, while migration studies using the nuclear genome are more recent.

The analysis of mitochondrial DNA occurred either by direct sequencing or, more commonly and more rapidly (30 years ago, at least), by restriction fragment length polymorphisms or RFLPs, which is described in Tool Box 3.1. RFLPs are easy to detect, even without sequencing, and certain variable sites in the mitochondrial genome were soon identified. Since there is no recombination with chromosomal genes, the entire mitochondrial genome comprised one haplotype, more properly referred to as a haplogroup.

Mitochondria are inherited exclusively from the mother in the cytoplasm of the ovum, so the haplogroup of your mitochondria indicate your maternal lineage for millennia. In general, changes in the mitochondrial genome are either highly deleterious (in which case, they are quickly lost) or selectively neutral; these neutral changes were the basis for recognizing different haplogroups. The polymorphisms are found primarily in two specific regions of the genome (which have no genes) called hypervariable regions 1 and 2. Based on these regions, there are more than 20 different mitochondrial haplogroups in humans, which have various relationships among themselves that arose by subsequent mutations. The L haplogroup, for example, has at least five subtypes referred to as L1, L2, L3, and so on. Most of these haplogroups are found only in some African populations; as with other types of genomic analysis, we see far more genetic diversity among African populations than in all of the rest of the world.

The differences among these haplogroups have been used to construct a phylogenetic tree, of the type discussed in Chapter 4. The hypothesized phylogenetic tree could be extended back to a single common ancestor (an ancestor of at least the 147 individuals used in the original analysis) who was estimated to have lived about 200,000 years ago, nicknamed the Mitochondrial Eve. It is postulated that the early hominids who descended from this common ancestor moved out of Africa and into the Middle East, and subsequently into Europe. All Europeans tested had the L3 haplogroup, so most non-African haplogroups are derivatives of L3.

Since that early study found seven haplogroups among modern Europeans (all derived from L3), these haplogroups were called the Seven Daughters of Eve in a popular book. The “daughters” were given nicknames based on the first initial of the haplogroup; the J1 haplogroup, which is common in the British Isles and Scandinavia, is called Jasmine, for instance. Subsequent analysis with additional data has suggested there may, in fact, be ten to 18 European haplogroups, rather than the seven originally proposed, which arose at various times and thus have different ages. The total number of surviving haplogroups worldwide could be as many as 29 or 30, depending on how the tree is constructed. There may be nine distinct mitochondrial haplogroups in Japan alone, for example, depending on how much similarity is required within a group.

Mitochondrial haplogroups are most useful for broad characteristics of heritage and have been widely used with old skeletons because mitochondrial DNA is fairly easy to obtain. For example, mitochondrial DNA analysis was used in 2012 to show that skeletal remains found in Leicester, England probably belonged to King Richard III who reigned only briefly from 1483 to 1485 but was immortalized by Shakespeare. Mitochondrial DNA represents only the maternal line, of course, so mitochondrial DNA analysis is only one a part of a person’s genetic heritage.

Y chromosomal DNA: what’s your name? Who’s your daddy?

The use of the Y chromosome as an analogous method to track paternal heritage began not long after mitochondrial analysis, as the tools for DNA amplification and isolation—particularly the use of PCR—improved. Most of the Y chromosome does not recombine with the X chromosome during meiosis, as discussed in Chapter 7. So, similar to mitochondrial DNA, the Y chromosome is passed to subsequent generations largely intact, with little exchange or mixing with other chromosomes. The differences that do arise are the result of intrachromosomal rearrangements that can occur within the Y chromosome itself and can be quite extensive, as well as any newly arisen mutations.

Because the Y chromosome is larger (59 Mb in humans) and has more sequence diversity than the mitochondrial genome, Y chromosome analysis provides more specificity than does mitochondrial genome analysis. There are more Y chromosome haplogroups than mitochondrial ones, and more individual variation as well. That said, Y chromosome analysis can be applied only to the males in the population, of course.

Mirroring mitochondrial analysis once again, Y chromosome analysis can be used to track human migration and founding populations. For example, an unusual Y chromosome polymorphism that was found among skeletal remains in modern Lebanon and Syria (the site of ancient Phoenicia) is also found among men living in seaports throughout the Mediterranean, including along the Atlantic coast of Portugal. This is consistent with the records of the Phoenicians as being great sailors in the ancient world.

Since surnames are also passed paternally among many western civilizations, there are ongoing genealogical projects to correlate British and Irish surnames (and other populations as well) with particular Y chromosome haplogroups. Many very common Irish and British surnames, such as Smith, Jones, Kelly, Murphy, and Brown, do not show a correspondence with a particular Y chromosome, indicating—not unexpectedly—that many men with the same last name are not genetically related to one another. Conversely, other surnames do have a shared Y chromosome haplogroup. Most individuals with the surname of Titchmarsh, Werrett, Herrick, or Attenborough have the same Y chromosome haplogroup as others with the same last name, suggesting that they all shared a male common ancestor many generations previously. The Y chromosome is a useful genealogical tool, since the spellings of names change much more often than the Y chromosome does, and DNA identifies genetic relationships better than names do.

Mitochondrial and Y chromosome DNA analysis for tracking migration and genealogies are so widely used that individual and national stories abound. Among the best known of these are the children fathered by Thomas Jefferson with his slave Sally Cummings and the Kohanim Y chromosome of Jewish priests. One historically interesting, if somewhat tragic, example of the use of mitochondrial DNA and Y chromosome analysis comes from villages in the Antioquia province in northwestern Colombia. Genetic testing of the current inhabitants of these villages finds that more than 90% of the maternal lineage is derived from a Native American mitochondrial haplogroup, not surprisingly. However, more than 90% of the paternal lineage is a Y haplogroup that is European and found primarily in regions in Spain, rather than among Native Americans. Similar results have been found in other South American locations, consistent with a genetic heritage of a Native American mother and a Spanish conquistador father.