Applications

Origins and Spread of Domesticated Animals and Plants

ADNA can uncover biogeography that has become blurred in modern genetics by subsequent events (e. g., specialist breeding, population movements). The available modern genetic and archaeological evidence for the domestication of cattle has pointed to at least two major sites of domestication in India and in the Near East (see Animal Domestication). Under this hypothesis, all present-day European breeds would be descendants of cattle domesticated in the Near East; however, aDNA from Italian aurochsen dated between 7000 and 17000 years BP suggest that there might have been local domestication events in Europe with introgression from European aurochs species.

A maize cob from the Ocampo Caves in Mexico dated to 3890 years BP was the first study of aDNA that looked at phenotype. Three genes (which control Plant architecture, storage protein synthesis, and starch production) were analyzed. aDNA showed the selection of traits during early domestication, and allowed estimation of when these desirable traits appeared (see Plant Domestication). Analysis suggested that the alleles typical of contemporary maize were already present in Mexican maize 4400 years ago, just a few thousand years after initial domestication from the wild grass teosinte.

Lost Genotypes

Mitochondrial DNA (mtDNA) has been analyzed from Late Pleistocene remains of brown bears and bison preserved in permafrost. Today, these species are found in distinct geographical regions, but aDNA showed them to have coexisted in a large diverse population throughout Beringia over 30 000 years ago, when the population’s genetic diversity began to decline. The implication for living population genetics is that much of the current distribution of mtDNA types might be due to relatively recent phenomena, such as the random loss of mtDNA lineages in small populations during the Last Glacial Maximum.

Evolution

ADNA has shown that evolution is more complex and dynamic than originally thought. aDNA allows direct estimation of the rate of nucleotide evolution of a population (mutation rate), by comparing individuals from different times. Lambert and co-workers measured the rate of mtDNA evolution by analyzing a large number of Adelie penguins from Antarctica. The data they produced allowed estimation of the molecular clock, which they found to be significantly faster than that previously used in theoretical models.

Ancient Communities

Cemetery studies have focused on genetic continuity between past and present human populations. mtDNA was analyzed from individuals from rural communities in Paucarcancha, Patallacta, and Huata near the famed site of Machu Picchu. The haplotype frequency data showed clear similarity to those of modern Quechua and Aymara people in the Peruvian and Bolivian highlands, and unlike those of pre-Hispanic individuals of the north coast of Peru, suggesting a strong genetic affinity between sampled late pre-Hispanic individuals and modern Andean highlanders.

Nuclear DNA sequences (autosomal and Y-chromo-some short tandem repeats) have also been obtained in cemetery studies. For example, DNA from a 2300-year-old Xiongnu population near Lake Baikal in northern Mongolia was compared with data from two contemporary Mongolian populations. Genetic similarities between the ancient and modern populations suggested that the succession of different Turkic and Mongolian tribes in what is now Mongolia was based on cultural rather than genetic exchanges.

Ancient Ecosystems

ADNA has been analyzed from Siberian permafrost sediments and from the soil of temperate caves in New Zealand, ranging in age from 10000 to 400 000 years. Fragments of different plant taxa could be identified from chloroplast DNA (angiosperms, gymnosperms, and mosses) and various animals including mammoth, bison and horse. Dramatic changes in the diversity and composition of Beringian vegetation during the Quaternary were apparent from the Siberian data. The temperate cave sediments from New Zealand also gave sequences of extinct species, including two species of ratite moa and 29 plant taxa characteristic of the prehuman environment.

Extinct Species

Perhaps the best known example is the woolly mammoth, which was the first Pleistocene animal to be sequenced. This is particularly notable because, recently, three independent groups have used cutting-edge technology to sequence the entire mitochondrial genome: one group sequenced 28 million base pairs of DNA in a metagenomics approach.

However, around 50 extinct animal species have been analyzed in order to relate them to living animals via molecular phylogenies, for example, Australian marsupial wolves, New Zealand moas, American ground sloths, and Hawaiian geese. The Australian marsupial wolf has been shown to be related to other Australian marsupials rather than to carnivorous marsupials in South America, suggesting that morphological features shared by marsupial wolves and South American marsupial carnivores may have evolved independently. Much of this has been based on mtDNA; however, nuclear DNA sequences have been determined from several Pleistocene animals and from plants preserved in dry environments. Recently, sex determination of moa samples using nuclear DNA sequences has revealed that several moa forms previously regarded as different species based on their morphology were, in fact, male and female birds of the same species.