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The nucleic-acid revolution started 31 years ago. The development of the second-generation sequencing (SGS) has allowed a higher throughput and lower price per sequenced base, opening the possibility to sequence ancient genomes, including epigenetics. The main SGS platforms are described in this review: i) Roche 454 Life Sciences, based on emulsion PCR (emPCR) and further pyrosequencing; ii) Illumina (bridge-amplification and subsequent reversible-terminator sequencing); iii) Life Technologies SOLiD (emPCR coupled with oligonucleotide ligation to interrogate DNA); and iv) Life Technologies Ion-Torrent-chip (emPCR, further using microchip pH-meters). Different ancient genomes (including viruses, microorganisms, plants and animals) have been sequenced. This has allowed to study the evolution of pathogens, domestication of microorganisms, plants and animals, paleodiets and paleoenvironments, including climate changes. Some hurdles and challenges must yet be overcome, but the steady technological advances in nucleic-acid isolation, sequencing and bioinformatics (together with higher computing power) promise a bright future for bioarchaeology in general, and paleogenomics in particular, allowing to analyze not just single genomes, but also to address ancient population genomics and evolution. [ABSTRACT FROM AUTHOR]

Glucose is preferentially stored as starch in plants. Thus, the remains of such polysaccharide may represent an invaluable source of archaeological evidence. The genomics, proteomics and metabolomics pathways can be also exploited to ascertain key events in phylogenetic processes. This includes the reconstruction of polyploidization events in plants and the identification of taxonomic positions. These developments are particularly relevant for the study of selection, evolution and domestication events of microorganisms, plants and animals. They include the adaptation to such food resource and the study of paleodiets and their implications for ancient and modern animals, including humans. [ABSTRACT FROM AUTHOR]