With the development of the Human Genome Project, a complete reference sequence of the human genome became available. As new sequencing platforms and bioinformatics tools were continuously developed, sequencing costs were reduced. The emergence of several genome projects was grounded in such developments, allowing the scrutinizing, at the genome level, of the present human genetic variation, the analysis of extinct species (such as the Neanderthal) as well as the study of non-human primates. A general characterization of the main genome projects with potential impact in the field of Biological Anthropology is performed in this chapter. Examples of studies which profited from the genomic data produced are also provided. As high resolution studies are becoming affordable and faster, anthropologists around the world are being challenged to benefit and exploit the data being generated from the several international large-scale genomic projects. If they are able to meet this challenge, traditional questions of anthropological importance can be addressed in a new and much more efficient way.

Sanger sequencing has been the standard method for mtDNA typing, however, over the past years, new technologies are rapidly evolving to overcome the limitations of the Sanger biochemistry approach. Massively parallel sequencing (MPS) or next-generation sequencing (NGS) technologies allow the sequencing of the entire mitochondrial genome at once, and the simultaneous sequencing of a large number of different samples. The technologies and software tools are rapidly evolving, and at the moment, several MPS platforms and different sequencing strategies are available, with their inherent advantages and limitations. However, the transition from traditional approaches to MPS-based tests demands for the development and validation of new routine procedures and optimized laboratorial protocols. When properly validated these systems can be applied to a wide range of fields spanning from Forensic and Population genetics to clinical casework. In this chapter, we present an overview of the currently available MPS sequencing methodologies for mtDNA analysis and discuss the advantages and limitations for each of the different applications.

Mitochondrial DNA (mtDNA) heteroplasmy is an almost universal condition in humans. The proportion of heteroplasmic mtDNA mutations that is heritable rather than accumulated during life has, however, remained almost unknown. The main goal of this work was to investigate the contribution of germinal versus somatic heteroplasmy, exploring its impact on health and aging. Blood samples from 101 individuals were previously used to generate full mtDNA sequences. Taking into account the embryonic origin of the tissues and the heterogeneity of site specific mutation rate of mtDNA robust criteria of heteroplasmy classification was applied. The mtDNA regions encompassing the 28 heteroplasmic positions detected in blood samples were sequenced in buccal epithelial samples as a reference from an alternative tissue with different embryonic origin. Based on the proposed classification data published by Li et al. (2015) was reanalyzed. Moreover, the predicted functional impact of non-synonymous mutations was evaluated. Most of heteroplasmies detected were germinal or somatic prior gastrulation and most of the somatic heteroplasmies were present in a single tissue. Somatic heteroplasmies were mostly present in older individuals, suggesting that they could be related to aging process. Three out of five non-synonymous mutations in heteroplasmy (all of them classified as germinal or somatic prior gastrulation) occurred in highly conserved positions, presenting a probability >60% of being deleterious. Although germinal heteroplasmies (or somatic prior gastrulation) can contribute to the development of disease and to the aging process, most of the heteroplasmies detected in both studies present a level of the alternative allele frequency below 60%, likely not affecting fitness and escaping selection.

The information contained into the human genome is the result of a historic process involving all the ancestors of a specific human being and it is a powerful tool for reconstructing human evolution. Key information about human evolutionary history can be robustly assembled from variation of the two haploid segments at uniparental transmission: mitochondrial DNA and Y chromosome. These two genetic systems are not subject to the rearrangement of recombination, and are inherited linearly through generations, having mutation as the only possible source of variation. In particular, the Y chromosome has been extensively studied for the study of human evolution. A major goal of the evolutionary research is not only to elucidate the pathways of the human peopling and the demographic changes that shaped the present populations, but also to date these events. For this aim, the recognition of a correct mutation rate is crucial. Genomic mutation rates can be estimated either by direct observation of mutations in present-day families (de novo mutation rate), by calibrating genetic variation against archaeological/historical records (evolutionary rate), or by using a sequence extracted from ancient human remains of known chronology. In order to test whether the same methodology could give consistent results when applied to different experimental contexts, we applied the evolutionary rate based upon archaeological evidence to two independent sets of data. Despite the striking difference in the absolute value of the substitution rate, the TMRCA of corresponding nodes in the phylogenetic trees obtained from the two databases are remarkably similar.

Genetic isolates correspond to subpopulations that have derived from a reduced number of individuals originally belonging to a main parental population, which have been submitted to isolation. Such subpopulations are widely acknowledged as important resources for the elucidation of the genetic basis of diseases. Mendelian diseases in particular have profited from gene finding strategies that use genetically isolated populations. In view of the success obtained for monogenic disorders, the scientific community was encouraged to use isolated populations with the purpose of analyzing complex diseases. In this chapter, the characteristics of human genetic isolates are addressed and the way by which they provide an advantage to gene finding studies is discussed. The implications of genomics for the efforts of gene identification using genetic isolates are also analyzed, and selected examples are provided. The availability of genomic data for isolated populations is currently providing in-depth insights into their structure, potentiating the use of research designs which are particularly suited for each isolate, thus increasing the chances of success of gene identification studies.

Genetic epidemiology is the discipline that studies the role of genetic and environmental factors in the origin of complex traits, behaviors and diseases. The major focus of genetic epidemiology is the analysis of the relative contribution of genes, environment and their interplay in human traits. Among others, twin studies have become an important tool to disentangle the different roles of genes and environment and to estimate heritability. Within the genetic epidemiology, the ecogenetics study the relationship between genetic and environmental factors and seek to understand both the vulnerability of different genotypes present in the population facing the same environmental risk factors (gene-environment interaction, GxE) and the influence of the individual's own genotype in the search of specific environments and/or risk factors (gene-environment correlation, rGE). There are numerous studies from quantitative genetics and molecular genetics that describe such GxE and rGE effects on the etiology of complex traits and disorders. However, it is important to consider the methodological requirements and limitations associated with these studies. Undoubtedly one of the challenges of genetic epidemiology in the coming years will be to combine the gene-environment studies (based on specific assumptions) with the huge amount of genomic data provided by new molecular approaches.

Since the arrival of the technology that permitted to recover and study ancient genetic material 30 years ago, its success has enjoyed steady growth, providing answers to a huge variety of fields, from personal identification to a better understanding of ancient human behavior, as well as the intricated evolution of our species or the recovery of genetic material from extinct ones. However, this field has also been accompanied by some handicaps which have complicated its improvement, as the damage that the individuals may have suffered over time and most notoriously contamination. A brief synthesis of the principal landmarks in this field’s history and the steps taken to overcome these problems are exposed in detail.

From the establishment of a first set of authenticity criteria to their progressive improvement in parallel with this field’s technology advances, the fight to overcome contamination has not ceased over the years. On its part, another problem at the time of recovering ancient genetic material can be caused by properties which may be inherent to the samples, as well as by their interaction with the elements where they are located. A summary from the evolution in these factors’ knowledge and the solutions that scientists have given them before the arrival of next-generation sequencing techniques is provided. Finally, a thorough description of the tissues from which ancient genetic material is recovered and the developments to do so from different source organisms is provided.

Methods to recover genetic material with the best possible quality have been improving in a similar way to the other areas in this field, culminating with the obtention of the first complete ancient mitogenome in 2001. However, with the arrival of next-generation sequencing in 2005, all these advances can be considered overcome. Using shotgun sequencing as basis and specially-designed microbeads to attach DNA, the advent of the palaeogenomics era has revolutionized the field. Also the enrichment techniques and the growing knowledge of ancient DNA diagenesis add significant achievements, but then again the roof of this technology has yet to be attained.

Human genome projects have been generating a vast amount of data which is impacting several areas, and forensic anthropology is no exception. In this chapter the interrelation between forensic anthropology and forensic genetics is highlighted, and the potential role that genomics can have in forensic science is addressed. The main sub-areas to which forensic anthropology can call the expertise of forensic genetics are listed and discussed. Genome-wide studies have recently started to be used to generate data which can efficiently aid forensic anthropologists; noteworthy, epigenetic analysis has also demonstrated its potential of application to questions that are posed to forensic anthropology. We argue that the partnership between forensic anthropology and forensic genetics is essential for stepping further in forensic sciences and that recent genomic tools have the potential to efficiently resolve questions left unanswered by genetics.