Genetic Genealogy: Understanding Ancestry DNA

The human body is miraculous. Twenty-three pairs of microscopic chromosomes, or complex protein-DNA structures, determine the recipe for what makes you, you. Sperm and eggs contain one copy of each of these twenty-three chromosomes. Each DNA strand contains a code, like a computer, for many different traits. When a sperm and an egg are generated in the parents during meiosis I, the chromosomes astoundingly pair up exactly right so the DNA with matching traits are linked together. Various factors determine what is translated when the DNA code starts building. For each trait, you may express the code received from your mother, your father, or a mixture of both, creating a brand new, 100% unique person.

Contents

Basics of DNA

DNA, short for deoxyribonucleic acid, is a chemical made up of molecules: groups of bonded atoms referred to as nucleotides.

Nitrogen bases

The most important part of these molecules is the four different nitrogen bases: adenine, thymine, guanine, and cytosine. For ease and simplicity, these nucleotides are often referred to by the first letter of their nitrogen base (A, T, G, and C). Have you heard of the film “Gattaca”? The movie revolves around the theme of genes and would be more appropriately referred to as “GATTACA.” When DNA is written out, it is just a long string of A, T, G, and C repeating over and over. The order that these “letters” (remember, they’re representing nucleotides) appear determines what that DNA will code for. This entire string of letters, or the complete genetic code, is called the genome. The human genome is approximately 3.2 billion nucleotides long. That’s 3.2 billion letters in a row!

Structure of DNA

You may have seen an image of DNA in the past. The standard form of DNA is called a double helix. The double helix is a winding structure made up of two strands. In essence, the double helix looks something like a ladder twisting around and around. Chemically, these strands are made up of alternating sugar and phosphate groups. There is a nucleotide on each strand at every rung of the “ladder,” or where the strands connect to each other. The two nucleotides are bonded together by something called a hydrogen bond. In order for a hydrogen bond to occur, a hydrogen molecule attaches to partially negative atoms on either side of it. A hydrogen bond is considered a relatively weak bond compared to normal bonds within molecules, though it is stronger than some other types of bonds. The important thing is that hydrogen bonds are capable of breaking with less effort than with other bonds.

Certain chemical rules require that the nucleotide adenine (A) on one strand pairs up with the nucleotide thymine (T) on the other, and similarly that the nucleotide cytosine (C) on one strand pairs up with the nucleotide guanine (G) on the other. Because of this, knowing the nucleotide sequence on one of the strands of the double helix will allow you to easily determine the nucleotide sequence on the other strand. DNA gets copied every time a cell divides itself. This is possible because of the unique double helix structure and because of the hydrogen bonds. During cell division, the DNA unwinds with the use of an enzyme, leaving two open strands as templates for new DNA. This process also happens when the DNA is in the process of making a protein.

Genes

Certain sections of nucleotides make up something called a gene (for example, GATTACA…….). These genes are what tell a cell what proteins to make, the building blocks of a body. As you know, there are many different versions of a single physical trait, such as hair color. This is because of alleles, or the subsections of a gene. Genes always have at least two alleles, but many genes have more alleles than that. Different alleles have varying degrees of dominance. For example, there is a blue eye allele and a brown eye allele. If a gene has two brown eye alleles that person will have brown eyes. However, the brown eye allele is considered dominant, so if a strand of DNA has one brown eye allele and one blue eye allele that person will still have brown eyes. Someone would need two copies of the blue eye allele to have blue eyes.

Chromosomes

Each cell normally, in a person’s body, contains all twenty-three pairs of chromosomes, except egg, gametes, red blood and skin cells. Chromosomes exist because DNA molecules are so long, they wouldn’t be able to fit into the cells on their own. Instead, the DNA is coiled up really tightly with a protein, making a chromosome. These twenty-three pairs of chromosomes, or forty-six in total, sit inside a cell’s nucleus. The nucleus is a small section sitting directly in the center of a cell.

The intricacies of what goes on in your DNA can be somewhat confusing, but the end result is the physical expression of the genome, or what a person looks like inside and out. Your genetic structure is called your genotype, and your physical structure is called your phenotype. A phenotype is everything that you can sense about a person, including invisible characteristics such as the sound of their voice and their behavior. While a person’s phenotype is based on their genotype, how their DNA gets expressed often relies on outward influences or things that happen to that person. It’s not nature vs. nurture; it’s nature and nurture.

Autosomal DNA or better-known as Ancestry DNA

What exactly determines whether you will be male or female?

It’s not as complicated as you may think. One single pair of chromosomes, called the sex chromosomes, control gender. There is an “X” chromosome and a “Y” chromosome which both contain completely different codes. Simply, when there are two “X” chromosomes in the pair, the body expresses female traits. When there is one “X” and one “Y” chromosome in the pair, the body expresses male traits. Because sperm and eggs contain only one-half of each chromosome pair, a sperm will either have an “X” chromosome or a “Y” chromosome – so it’s your dad that technically determines your gender! There are many traits coded into the sex chromosomes’ DNA strand, not all of which are traditionally associated with a specific gender. For example, color-blindness occurs when there is a mistake in the color code in the “X” chromosome. Because females have two “X” chromosomes, if one color code is normal, she won’t be color-blind. However, males only have one “X” chromosome and are out of luck if that one contains a mistake.

The twenty-two chromosomes that are not sex-linked are referred to as “autosomal chromosomes” and likewise contain “autosomal DNA.” Each strand of DNA has a different number of genes. The autosomal chromosomes are numbered in order from the one with DNA containing the highest number genes (Chromosome 1 has approximately 2,800 genes) to the one with DNA containing the least number of genes (Chromosome 22 has approximately 750 genes). While there is no official abbreviation for autosomal DNA, it can often be referred to as atDNA or auDNA for ease.

Because atDNA contains information from both the mother and father, genes can be traced back up family trees in both directions. Genetic tests that use the “Y” sex chromosome can only follow the male line. Similarly, tests on mitochondrial DNA (a form of DNA inherited from the mother) can only follow the female line. AtDNA can be used to estimate your ethnic percentages based on the ethnicities of your relatives.

Ancestry DNA testing

In order to use atDNA to dig into someone’s ancestry, scientists had to come up with something called Ancestry Informative Markers, or AIMs. Researchers collected DNA from around the world and evaluated the composition of alleles. They found that at populations around the world share common allele frequencies. At certain “loci,” or locations in someone’s DNA, on average a population will share a common allele. Because of this, AIMs can be used to sort people into genetic categories. By evaluating DNA at AIM loci, scientists can determine what population that person’s specific gene likely derived from. At first, AIMs could only identify between European, Asian, and African. However, now that technology has evolved and more research has been done, the categories got more specific. They now include direction, such as Northern European vs. Southern European, or East Africa vs. West Africa.

If you look at someone you can often make generalizations about their ethnicity based on how they look, although it’s very difficult to pinpoint exactly where someone or their ancestors came from. Looking at DNA can get more specific answers. However, DNA can also blur the lines when it comes to race. Some ethnic groups may be so closely related that it’s difficult to distinguish between them when DNA is tested. More work and more research are necessary in the field of DNA testing.

Another way atDNA can be tested is with something called Codis Markers. These markers are generally used more often to compare close relatives or simply distinguish people from each other. This type of test can be used to test for paternity and whether or not two people are siblings. It is also useful for forensics because it can be used to identify a specific person. The test is very specific to one or a few people and is not compared to larger groups to determine ethnicity. The results of the test are output as numbers. By itself, someone’s results can be used as a unique number “fingerprint.” When comparing the results of a few people, matches between the numbers will determine relatedness.

Just to make things all the more confusing, DNA is not inherited in equal parts from your ancestors. You would expect to receive 25% of your DNA from each of your grandparents. What traits are passed on to each new generation is completely random, however, so therefore someone may only get 10% of the DNA from one grandparent and 90% from another. Eventually, DNA from your ancestors will disappear when it is not selected to be passed on. This makes ancestral testing a bit complicated. Since you and your siblings receive different genes from your ancestors, you most likely will end up with different ethnicity percentages. In addition, AIMs only represent a small amount of your genome (or overall genetic structure). Tests are also limited, and may have trouble distinguishing between certain populations, such as Scandinavian and British. Therefore, tests on atDNA are only estimations of someone’s ancestry. Y-Chromosome and Mitochondrial DNA testing can help provide a clearer picture.

Evolutionary genetics and population genetics

There are a few subsets of genetics that specifically look at how genes are passed on over time. These are evolutionary genetics and population genetics. Evolutionary genetics stems from Darwinian evolution. Charles Darwin, as you may know, wrote about natural selection. Natural selection has come to be known as “survival of the fittest,” but it’s a little more involved than that. The simple definition is that natural selection is a process that occurs because certain living organisms are better adapted to their environment than others. These better-adapted organisms survive better than the others and therefore have or produce more offspring. From a genetic standpoint, this means the better-adapted organisms are passing on their genes. Evolution occurs when the frequencies of genes in a population of organisms changes over time. Natural selection is just one method of evolution.

Population genetics is an even more specific version of evolutionary genetics. Evolutionary genetics looks at the big picture of evolution, while population genetics looks at the change in genes within populations. This may be a change over space (physically moving around) or over time. There are many different factors that play into what organisms survive and when. People devote their entire careers to studying all the different methods of evolution and what factors into those methods. The one thing that most of the methods of evolution share, however, is that they are outwardly putting pressure on living organisms. A lot of evolution has to do with the environment that an organism is living in.

Genetics, particularly evolutionary and population genetics, requires the use of a lot of math. There are many different mathematical formulas to help scientists determine how genes and alleles will likely change over time. There is, however, a simpler way to estimate the likelihood of alleles appearing in offspring. The method, somewhat like a multiplication table, is called a Punnett Square. In order to best understand how the Punnett Square is used, you should know that alleles are often referred to by single letters (not to be confused with A, T, C, and G). Dominant alleles are capitalized while recessive (non-dominant) alleles are lower case.

Punnett Squares

Punnett Squares look at a single gene at a time. It is simplest to do a Punnett Square when there are only two alleles for that gene, but the method can be used when there are more. For a two-allele gene, draw a box, and then draw two lines to split that box into four smaller boxes. On one edge, write the two alleles possessed by one parent. On the other edge, write the two alleles possessed by the other parent. Then, in each of the four boxes, write the combination of alleles that line up from each parent. By knowing which allele is dominant, you can determine what phenotype (or physical expression) the offspring would have with each of those combinations of alleles. The result is a probability, or what phenotype you should expect from offspring of those two parents. See the figure below for a physical representation.

B = Brown eyes (dominant)

b = blue eyes (recessive)

Punnett Square

In this scenario, we would expect 2 out of 4, or 50%, of these parents’ offspring to have brown eyes, and 2 out of 4, or 50%, of the offspring to have blue eyes. Recall these are probabilities and are not guaranteed.

This directly relates back to the problem of only receiving some atDNA from each of your ancestors. The farther back you look, the less likely you are to find the allele that exists in you today. Alleles change ever generation, so you might say that your family tree – and its ethnicity – evolves over time. As we touched on at the beginning of this article, you are a unique person. You have a completely unique set of alleles that make you who you are. However, there is a way that makes your ancestors’ alleles more likely to appear in your today: inbreeding.

Often, the recessive alleles are considered the incorrect, or broken, alleles. They are the alleles that aren’t meant to express themselves. It’s lucky that we have at least two alleles so the dominant trait can beat out the weak trait. Since there are only two parents to choose alleles from, siblings are likely to share quite a number of their alleles. For example, in the Punnett Square above, every single offspring will end up with a recessive blue eye allele. When two people who are unrelated have offspring, there is a completely random chance both of them would carry the same recessive alleles. If two people who are related have offspring, there is a much higher chance the same recessive alleles they carry will meet and be expressed. If you look at the Punnett Square above, if the two offspring with blue eyes had offspring of their own, the probability of them having blue-eyed offspring jumps to 100%.

Autosomal DNA testing comparison

Because of these high probabilities of sharing alleles between family members, atDNA is commonly used to discover how related two individuals are to each other. In order for this test to work, at least two people need to take it. The various companies that perform atDNA family finding tests take your atDNA and determine what it looks like at your AIMs. The companies then compare these results to the results of other people who have taken their tests. They look for matching segments. Some matches may be coincidental, but the more identical segments you have with someone, the more likely you are to be related to them. Equations from population genetics can help determine the probability that those matches occurred because of chance or not. The problem with these tests is that they rely on other people having taken the test. If they don’t have someone’s DNA to compare to yours, they can’t tell you if you’re related to them. There are currently three companies offering this testing: Family Tree DNA, 23andMe, and Ancestry.com.

There are differences between these three testing companies that you will want to know if you consider doing an atDNA test. If you are primarily interested in genealogy, Family Tree DNA and 23andMe are the best options. Family Tree DNA compares your atDNA results to all their customers’ atDNA results. However, their test cannot tell if a segment is half-identical or fully identical, which is important if you are specifically looking at siblings. Full siblings will have some fully identical segments. For sibling comparison, you will want to go with 23andMe. 23andMe is also a good choice if you are interested in your ethnicity, or your personal racial makeup. While the results can be simple (100% European for example), they are the most scientifically sound and least confusing.

Conclusion

DNA is vital to a lot of research done in the broad field of Biology. However, there is still a lot we don’t understand. We are limited by computer power, brain power, and time. At this point, we don’t have the capability of sequencing the entire genome of large groups of people. There could be a lot we’re missing about evolution, ethnicity, and how genes change over time around the world. We have made a lot of progress with atDNA, though, leading us to open up a world where we can make reasonable assumptions about where people come from and who they are related to. Not only is this information interesting to us individually, it is very important to the research being done on how our ancestors moved around the Earth. We have made a lot of progress so far, and there is a bright future ahead of us.

References

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