As humans, we have a graspable identity that has been shaped by our individual and collective attempts to seek answers to fundamental questions: Who am I? Where did I come from? Where am I going? Where and to whom do I belong, and how can I help myself and others? The persistence of such questions may signal the insatiability of our human curiosity, but they also offer evidence of our possibly endless search for substantive, finite meaning. We yearn to identify who we are and to be part of something greater than our own limited individuality. This desire leads people to draw strong, even vicious, us-versus-them boundaries in political and social life. But it is also a spiritual wish to connect to all of humanity, indeed to all of life and the cosmos, and to take benevolent action accordingly (Figure 1.1, chapter opener). Even when answers to our questions about identity prove inconclusive, changeable, or otherwise unsatisfying, our search continues apace.

Evolutionary genetics attempts to make evolutionary theory mathematically explicit through measuring change at the gene level, but once data have been gathered, modeling and interpretation – albeit contextual and thus limited – must be applied. In this chapter, I take a closer look at population modeling, moving from measurements and data to the investigation of two mathematical modeling strategies at the heart of genomic calibrations and analyses of human populations: variance partitioning and clustering analysis.

Modern human evolutionary genomics applies natural scientific knowledge to address ancient and fundamental Why? questions, enabling us to deepen our philosophical reflection on identity and futurity. But to understand contemporary human evolutionary genomics, we must comprehend the field’s explicit and implicit connections to its origins and early development. By delving into the basic theoretical outline and historical sources of human evolutionary genomics, we become more familiar with the layered and fractal history of Homo sapiens.

The era of forensic DNA typing began in the 1980s when ABO and isoenzymes were the forensic tools for biological identification. As was the case with ABO blood grouping, DNA profiling was adapted from research in molecular biology. However, migration from the research laboratory to the forensic laboratory involves far more than buying new equipment. Forensic methods and techniques must satisfy two diverse communities – the scientific and the judicial. There is a common misconception that science and justice both seek “truth” and are natural partners. This assessment is oversimplified. At best, the disciplines manage to work together in a strained relationship. Before we move on to the science of DNA profiling, we need to explore how DNA found acceptance in the courts.

When a new scientific method is employed in a case, the courts must decide whether the data will be admitted into evidence that will be seen by those who will pass judgment, such as a judge or jury.

DNA profiling of STR loci is a mature technology. Improvements continue in sensitivity and additional STR loci, but the process, kits, and instrumentation are established. Courts, police, and the legal system accept and rely on DNA evidence, and databases continue to grow. However, this does not mean that the field has become static. Research continues, and newer concepts are being evaluated and adopted by the forensic community. Some of these are evolutionary, while others could be revolutionary.

We have come a long way in a short time. From the first use of DNA typing for a criminal investigation in 1986 to now, over 35 years have passed. Those years have brought a revolutionary change in human identification, from ABO blood typing to analysis of complex mixtures, probabilistic genotyping software, and investigative genetic genealogy. Forensic DNA typing now applies to STRs (still the primary method), Y-STRs, mitochondrial DNA, and SNPs. We have law enforcement databases and consumer databases that are used in current and cold cases. We have seen how portable DNA instruments can be used in mass fatalities and police booking stations.

There are several key takeaways from this journey, including the need to correct several common misunderstandings, as summarized in the next section.

So far, we have focused on DNA types in which one allele is from the father and one from the mother. However, three other sources of DNA come from only one parent, and all can be employed in forensic testing. One is mitochondrial DNA (from the mother in all her children), and the other two are STR sites on the Y chromosome (from the father in his sons) and STR sites on the X chromosome (from the mother in her sons). These DNA sources are lineage markers, since they can be traced back generations through our family trees. Lineage markers are valuable in missing person cases where DNA from the person of interest is not available. Mitochondrial DNA (mtDNA) has been used in historical cases, such as identifying soldiers killed in past conflicts. We will explore these and other examples in this chapter.

Forensic samples are among the most complex encountered. Blood is best known, but other biological matrices also carry genetic information. Cheek swabs (buccal swabs) collect cells from the inside of the mouth and have the advantage of being a non-invasive sample collection compared to a blood draw. Hair, depending on the presence of the root, is amenable to DNA typing. Semen, vaginal fluids, and vaginal swabs are collected in sexual assault cases. Any surface on which biological fluids (blood, oral fluid, vaginal fluid, etc.) are deposited becomes a potential DNA source.

The initial deposition (called the primary transfer) occurs from a person to a surface. It is the deposition of blood, saliva, semen, or other biological substance directly from the body onto a surface. This process could be a victim’s blood dripping onto an assailant’s clothing, saliva on a cigarette, or seminal fluid on a bedsheet.

Forensic DNA typing was developed to improve our ability to conclusively identify an individual and distinguish that person from all others. Current DNA profiling techniques yield incredibly rare types, but definitive identification of one and only one individual using a DNA profile remains impossible. This fact may surprise you, as there is a popular misconception that a DNA profile is unique to an individual, with the exception of identical twins. You may be the only person in the world with your DNA profile, but we cannot know this short of typing everyone. What we can do is calculate probabilities. The result of a DNA profile translates into the probability that a person selected at random will have that same profile. In most cases, this probability is astonishingly tiny. Unfortunately, this probability is easily misinterpreted, a situation we will see and discuss many times in the coming chapters.

The last chapter outlined the basic concepts of mixture analysis. Now we move on to the much more challenging situations arising from low-level DNA samples and complex mixtures. These topics go together. Early DNA methods such as RFLP and initial PCR methods were less sensitive (which means they were unable to detect very small quantities of DNA) than today’s techniques. As a result, DNA present in tiny quantities was not seen. Now the technologies afford much better detection, which is a mixed blessing. Rather than simply detecting the DNA from the major contributor(s), now trace levels of DNA can be recovered and typed, and not all of it is pertinent to the crime under investigation. Very small amounts of DNA, much less than in typical samples, are referred to as low copy number (LCN) DNA.

Low copy number and complex mixtures are related.