Archaeogenetics

Principles of Genetics

Deoxyribonucleic acid (DNA) refers to the sequence of nucleotide bases (adenine, cytosine, guanine, and thymine) that join together in a long molecular chain and form genomes - the instruction code for building and running biological organisms. The 3 billion bases of the human genome are divided into 24 chromosomes consisting of 22 autosomes and, either, two X, or one X and one Y, sex chromosomes. An additional piece of DNA, mitochondrial DNA (mtDNA), contains slightly more than 16 500 bases and resides separate from nuclear DNA.

Nearly all of the DNA sequence is identical in all humans, but about 0.1% varies at locations across the genome, mostly as single nucleotide polymorphisms (SNPs). These SNPs, where one nucleotide has spontaneously changed, or mutated, to another, are inherited generation to generation and are the fundamental data for reconstructing ancestry.

Ancient DNA analysis refers to the extraction of genetic material from plants, coprolites, humans, and nonhuman animals from museum or archaeological specimens. The retrieval and analysis of ancient DNA is considerably more difficult than of modern DNA. Not only is it fragmentary, due to degradation, but extracting uncontaminated genomic material requires exacting procedures. Thus, much focus has been on possible sources of contamination, methods to overcome biochemical inhibitors to sequence amplification, and ways to authenticate the ancient DNA sequences.

Genetics (DNA and molecular markers) gives access to information at the individual, intrapopula-tional, and interpopulational levels. Comparison of the genetic profiles of multiple individuals is a means for determining biological distance and thus kinship. Comparing collections of genetic profiles from different populations reveals their relationships in evolutionary terms and their diachronic associations. Anthropological genetics proffers the capacity for inferring kinship structure, population movements, and the biological relatedness of populations across regional and continental distances directly from archaeological skeletal remains. Understanding the populational, genetic, and social structures of ancient cultures can improve our interpretations of human migrations, our models of the social structures and relationships among cultural divisions, and the demographic structures of past societies. Since ancient societies, especially prestate ones, organized their labor, economic, political, and social institutions and activities by age, sex, kinship, and social rank, our models and reconstructions are dependent on the quality of our knowledge of genetic and social relationships.

Differences among people according to their sex and kinship are central to anthropological models of the evolution of ancient societies, especially the political and economic structures. Reconstruction of cultural institutions in archaeology is often performed by ethnographic analogies to settlement survey and excavation data. Rarely does direct evidence exist for examining kinship models from archaeological remains. Individual relatedness among people in households, residential groups, and communities would provide reconstructions with direct evidence for the kinship organization of the society under study. Genetic relations are difficult to reconstruct, except in unique circumstances where written records exist and, even then, relationships are only recorded for the uppermost levels of society, so the vast majority of people remain anonymous. With the recent advent of ancient DNA techniques, we have the potential to reconstruct kinship ties for all social statuses.

Expertise in genetics and nucleic acid extraction, polymerase chain reaction (PCR) amplification, sequencing or genotyping of informative genetic components (e. g., mitochondrial DNA, microsatellites, and X or Y chromosomes), statistical analysis, and phylogenetics is required to reconstruct the complex evolutionary history of organisms. Deoxyribonucleic acid is extracted and authenticated from archaeological, museum, and fossils samples. Genetic reconstruction can then proceed to tackle the questions of the genetic structure of extinct species in relation to contemporary species, solve the phylogenetic relationships within our genus Homo, and uncover kinship structure and the biological sex of individuals buried in cemeteries, to infer the routes and times of human movements, and determine the genetic composition of microorganisms.

Evolutionary Relationships

Key to studies of this type is an understanding of phylogenetics, tokogenetics, and coalescent theory. Phylogenetics is the science of classification, or taxonomics, and representation of the biological and genealogical relationships among biological entities arising through evolution. Phylogenetic analysis is a mathematical approach based on computation of the similarities and differences among sampled populations for inferring or estimating evolutionary relationships, estimating the time of divergence between entities, and chronicling the series of events along lineages.

The evolutionary history of taxa may be represented as trees. Typically, hierarchical relationships are shown as a schematic tree comprised of nodes connected by branches. A node indicates the stage at which two or more branches diverge. Thus, the evolution from ancestors (internal nodes) to extant descendants (terminal nodes, tips, leaves, or operational taxonomic units) is estimated from the variations in a set of characters. In molecular phylogenetics, the characters are DNA or protein sequences.

Groups within a tree are either monophyletic, poly-phyletic, or paraphyletic. A clade or monophyletic group is a natural taxon in which all members are derived from a unique common ancestor with respect to the entire tree, have inherited a common set of traits, and thus have a shared evolutionary history. A group excluding some of its descendants is paraphyletic. In opposition to monophyletic is polyphyletic, in which a group shares a common ancestor with another group and probably represents an incomplete clade.

Networks best represent intraspecific relationships (tokogeny). This is because species phylogenies are the result of reproductive isolation and population fissioning over longer time periods during which mutation combined with population divergence led to the fixation of some alleles and to nonoverlapping gene pools. In contract, intraspecies genealogical relationships arise by the sexual reproduction of fewer, more recent mutations and recombination. Evolutionary processes occurring among sexual species are hierarchical because an ancestral species gives rise to two descendant species. Within sexual species the processes are nonhierarchical because two parents combine their genes resulting in offspring.

Tracing the merging of ancestral lineages backwards through time is coalescence. Models of DNA polymorphism in a population include not just mutation, but the genealogy of sampled sequences as determined from the additional sources of variation - recombination and coalescence. Under coalescent theory, sampled lineages are treated as randomly picking their parents, tracking backwards through time until their lineages coalesce into a single lineage of the most recent common ancestor. This approach is more appropriate when the questions involve migration, or estimate or model other parameters such as population size or bottlenecks, admixture, or other demographic features impossible to address with phylogenetic methods.

Polymerase Chain Reaction

The advent of the PCR and associated molecular biological laboratory advances have been the foundation for successful work in archaeogenetics. Since only tiny amounts of genetic material can be collected from specimens and only short stretches of the genetic code can be read at a time, a method for copying specified chunks of DNA is required. PCR, though a thermochemical reaction, is the process of amplifying (repeated copying) unique DNA sequences from a mixture of sequences with the use of primers (short oligonucleotides designed to match and prime DNA sequences). The amplified DNA can then be analyzed further with sequencing instruments that read the nucleotide code (A, C, G, or T), or with methods to test for known genetic markers.

Mitochondrial DNA

The majority of ancient DNA studies are based on the amplification of multicopy DNA sequences like mtDNA and chloroplast DNA. The mtDNA genome has been fundamentally useful to ancient genetics because thousands of copies exist per cell while nuclear genes have only two copies per cell, it is only maternally inherited, it is haploid (having one set of genes), and does not undergo recombination as it is passed intact from mother to child. An extensive understanding of its worldwide diversity has been developed, particularly in terms of stable polymorphic sites or haplogroups, from which maternal lineages can be identified and related to populations that are divergent from each other or that share hap-lotypes. Similarly, paternal lineages may be traced via the Y chromosome, also uniparentally inherited without recombination, but it has only one copy compared to the thousands of copies of mtDNA per cell. Since the DNA of living populations only relates to surviving descent lines, ancient DNA holds the potential to uncover extinct lineages.

Archaeogenetic Applications

Successful analysis has been performed on remains consisting of osseous matter, hair, teeth, and fossils. Determining the point of origin, when the process began, and sometimes from which wild ancestor domesticated plants and animals were derived has been advanced by ancient DNA studies. The genetic changes (e. g., reduced variation) occurring from the process of long-term selection for domestication and comparison of ancient DNA against modern relatives has provided insight into the domestication history of dogs, cattle, horses, goats, squash, and maize, among others. Ancient DNA studies provide a powerful, direct appraisal of genetic relationships among extinct species and to their present descendants.

Pleistocene animal genetic history Several extinct Pleistocene animals have had their DNA analyzed, including mammoth, mastodon, ground sloth, cave lion, and cave bear. The population history and phylogeography of species can be traced over time when many individuals have been preserved. For example, ancient DNA analysis of Late Pleistocene brown bears indicated that the mtDNA brown bear lineages have changed from a pattern of coexistence in a single area 35 000 years ago to the modern pattern of lineages distributed into different geographical regions worldwide. In another study, ancient mtDNA retrieved from moas as old as 3500 BP showed that Australian emus and cassowaries were closer relatives to moas than to kiwis. Apparently, flightless birds colonized New Zealand twice, once by ancestors of moas and independently by ancestors of kiwis.

Human ancestral genetic history Resolving the genetic affinities of Neandertals and contemporary hominids is central to two competing theories of modern human origins - the replacement model and the multiregional model. Under a theory of replacement, modern humans rapidly replaced archaic hom-inid forms such as Neandertals as they spread from Africa throughout western Asia. Alternatively, under the multiregional model, genetic exchange occurred and continuity existed between archaic hominids and modern humans. mtDNA segments amplified from Homo neanderthalensis remains shows them to be genetically distinct from contemporary humans and phylogenetically outside the mtDNA variation of living humans. As estimated from the population genetic analysis of mtDNA sequences retrieved from Neandertal specimens, their genetic contribution to early modern humans appears to be less than 25% and very likely Neandertals went extinct without contributing mtDNA to living humans. The mtDNA lineage that leads to Neandertals diverged about 500 000 years BP, while the common maternal ancestor of Homo sapiens sapiens probably lived around 170 000 years BP. Thus, from the mtDNA evidence, a recent African origin and little genetic intermixing is supported.

Cultivar genetic histories The evolutionary histories of cultivars such as maize (Zea mays), grape (Vitis vinifera), Cucurbita (squashes, pumpkins, and gourds), and olive (Olea europaea L.) are being resolved in the light of new DNA studies and phylogenetic analysis. The timing and nature of plant domestication in the Americas has been a major research focus. The genus Cucurbita consists of a dozen or more domesticated and wild species distributed throughout the Americas. Before European contact, six different species were domesticated and formed important sources of food in Native American economies. Molecular evidence (chloroplast DNA and mtDNA) from extant specimens indicates that domestication of C. pepo occurred twice; once, possibly in southern Mexico 10 000 BP or earlier, as a lineage that includes pumpkins among its members, and again, another lineage with members including acorn squash and ornamental gourds, was domesticated possibly in the Ozark Mountains around 5000 BP.

Peopling of the Pacific islands One of the more perplexing and complex mysteries of prehistory has been the timing and pattern of the settlement of the islands of the Pacific Ocean. One approach is to study commensal species. The Pacific rat (Rattus exulans) is an especially useful species because its distribution ranges from Southeast Asia across the Pacific Ocean to Easter Island, its remains are associated with the Lapita cultural complex and later Polynesian settlements, they do not swim, thus required human transportation, and the species is distinct from the European rats (R. rattus and R. norvegicus) introduced later.

Variation in extant rat population mtDNAs throughout Oceania identified pathways taken by the human settlers as they carried the Pacific rat with them for food beginning 40 000 years BP. Three distinct hap-logroups of R. exulans have been identified, lending strongest support to a model of Lapita settlement and interaction with indigenous inhabitants over a period 6000-3000 years BP, along a voyaging corridor from eastern Indonesia to the Bismarck and Solomon Islands.

See also: Archaeometry; Chemical Analysis Techniques; DNA: Ancient; Modern, and Archaeology; Metals: Chemical Analysis; Primary Production Studies of; Migrations: Australia; Pacific; Neutron Activation Analysis; Organic Residue Analysis; Stable Isotope Analysis; Trace Element Analysis.